From 8176ba9441d45b7610823f99b2032e6ce4704bc1 Mon Sep 17 00:00:00 2001
From: JuliansGHUB1 <105456402+JuliansGHUB1@users.noreply.github.com>
Date: Tue, 9 Jan 2024 09:29:35 -0500
Subject: [PATCH 1/6] recent changes
---
resource.iml | 56 ++++++++++++++++++
.../org/panda/resource/UniProtSequence.java | 42 ++++++++++++-
.../panda/resource/CancerGeneBushman.class | Bin 0 -> 4937 bytes
.../org/panda/resource/CancerGeneCensus.class | Bin 0 -> 5677 bytes
target/classes/org/panda/resource/ChEBI.class | Bin 0 -> 5966 bytes
.../classes/org/panda/resource/Download.class | Bin 0 -> 6451 bytes
.../org/panda/resource/FileServer.class | Bin 0 -> 5172 bytes
target/classes/org/panda/resource/GO.class | Bin 0 -> 17038 bytes
.../org/panda/resource/GWASCatalog.class | Bin 0 -> 5318 bytes
target/classes/org/panda/resource/HG37.class | Bin 0 -> 4324 bytes
.../classes/org/panda/resource/HGNC$1.class | Bin 0 -> 520 bytes
target/classes/org/panda/resource/HGNC.class | Bin 0 -> 8589 bytes
.../org/panda/resource/KinaseLibrary.class | Bin 0 -> 7015 bytes
target/classes/org/panda/resource/MGI.class | Bin 0 -> 5378 bytes
.../MGIVertebrateHomology$Organism.class | Bin 0 -> 2245 bytes
.../resource/MGIVertebrateHomology.class | Bin 0 -> 4706 bytes
.../panda/resource/MSigDB$NameFilter.class | Bin 0 -> 239 bytes
.../classes/org/panda/resource/MSigDB.class | Bin 0 -> 13479 bytes
.../MatrixOfValuesDatasetReader.class | Bin 0 -> 6838 bytes
.../classes/org/panda/resource/OncoKB.class | Bin 0 -> 9139 bytes
target/classes/org/panda/resource/PAM50.class | Bin 0 -> 6507 bytes
.../org/panda/resource/PCPathway.class | Bin 0 -> 27899 bytes
.../resource/PCPathwayHGNC$Pathway.class | Bin 0 -> 1803 bytes
.../org/panda/resource/PCPathwayHGNC.class | Bin 0 -> 7459 bytes
.../org/panda/resource/PCPathwayUniprot.class | Bin 0 -> 656 bytes
.../classes/org/panda/resource/PiHelper.class | Bin 0 -> 6999 bytes
.../classes/org/panda/resource/Pubmed.class | Bin 0 -> 2964 bytes
.../org/panda/resource/ReactomePathway.class | Bin 0 -> 8645 bytes
.../panda/resource/ResourceDirectory.class | Bin 0 -> 1263 bytes
.../resource/SignedInteractionText.class | Bin 0 -> 4612 bytes
.../resource/SiteMappingMouseToHuman.class | Bin 0 -> 5669 bytes
.../resource/SiteMappingRatToHuman.class | Bin 0 -> 4107 bytes
.../org/panda/resource/UniProtSequence.class | Bin 0 -> 7507 bytes
.../autismdatasets/DenovoDB$DataFilter.class | Bin 0 -> 377 bytes
.../DenovoDB$DataFilterEnum.class | Bin 0 -> 12841 bytes
.../autismdatasets/DenovoDB$Entry.class | Bin 0 -> 3916 bytes
.../resource/autismdatasets/DenovoDB.class | Bin 0 -> 34355 bytes
.../IossifovDataset$DataFilter.class | Bin 0 -> 412 bytes
.../IossifovDataset$Entry.class | Bin 0 -> 1074 bytes
.../autismdatasets/IossifovDataset.class | Bin 0 -> 11436 bytes
.../resource/autismdatasets/SFARI$Entry.class | Bin 0 -> 1194 bytes
.../panda/resource/autismdatasets/SFARI.class | Bin 0 -> 8918 bytes
.../resource/network/ActivityNetwork.class | Bin 0 -> 13210 bytes
.../org/panda/resource/network/IPTMNet.class | Bin 0 -> 6731 bytes
.../panda/resource/network/NetworKIN.class | Bin 0 -> 5823 bytes
.../resource/network/PathwayCommons.class | Bin 0 -> 9512 bytes
.../resource/network/PhosphoNetworks.class | Bin 0 -> 2976 bytes
.../resource/network/PhosphoSitePlus.class | Bin 0 -> 10769 bytes
.../org/panda/resource/network/RhoGEF.class | Bin 0 -> 2048 bytes
.../resource/network/SignedMetabolic$1.class | Bin 0 -> 849 bytes
.../resource/network/SignedMetabolic.class | Bin 0 -> 2799 bytes
.../org/panda/resource/network/SignedPC.class | Bin 0 -> 9631 bytes
.../resource/network/SignedPCNoTransfac.class | Bin 0 -> 2983 bytes
.../panda/resource/network/SignedREACH.class | Bin 0 -> 3005 bytes
.../org/panda/resource/network/TFactS.class | Bin 0 -> 5540 bytes
.../org/panda/resource/network/TRRUST.class | Bin 0 -> 4434 bytes
.../resource/network/UniProt$Relation.class | Bin 0 -> 619 bytes
.../resource/network/UniProt$UPHandler.class | Bin 0 -> 5557 bytes
.../org/panda/resource/network/UniProt.class | Bin 0 -> 4086 bytes
.../proteomics/MDACCFormatRPPALoader.class | Bin 0 -> 6118 bytes
.../resource/proteomics/RPPAIDMapper.class | Bin 0 -> 10366 bytes
.../signednetwork/ConflictResolver.class | Bin 0 -> 9728 bytes
.../ConflictResolverSimple.class | Bin 0 -> 8857 bytes
.../ControlSignConstraint$1.class | Bin 0 -> 902 bytes
.../ControlSignConstraint$Sign.class | Bin 0 -> 1346 bytes
.../signednetwork/ControlSignConstraint.class | Bin 0 -> 1691 bytes
.../panda/resource/signednetwork/EN1.class | Bin 0 -> 1280 bytes
.../panda/resource/signednetwork/EN1C.class | Bin 0 -> 935 bytes
.../panda/resource/signednetwork/EN2.class | Bin 0 -> 1280 bytes
.../panda/resource/signednetwork/EN2C.class | Bin 0 -> 935 bytes
.../panda/resource/signednetwork/EP1.class | Bin 0 -> 1402 bytes
.../panda/resource/signednetwork/EP1C.class | Bin 0 -> 935 bytes
.../panda/resource/signednetwork/EP2.class | Bin 0 -> 1412 bytes
.../panda/resource/signednetwork/EP2C.class | Bin 0 -> 935 bytes
.../panda/resource/signednetwork/GN1.class | Bin 0 -> 2597 bytes
.../panda/resource/signednetwork/GP1.class | Bin 0 -> 2598 bytes
.../GTPChangeConstraint$Type.class | Bin 0 -> 1334 bytes
.../signednetwork/GTPChangeConstraint.class | Bin 0 -> 3130 bytes
.../resource/signednetwork/Generator.class | Bin 0 -> 15732 bytes
...ionByBindingMiner$IsSubsetAndReverse.class | Bin 0 -> 2323 bytes
.../InhibitionByBindingMiner.class | Bin 0 -> 2364 bytes
.../resource/signednetwork/Inhibits.class | Bin 0 -> 1324 bytes
.../signednetwork/NotLessDirect.class | Bin 0 -> 1631 bytes
.../panda/resource/signednetwork/PN1.class | Bin 0 -> 2213 bytes
.../panda/resource/signednetwork/PN1C.class | Bin 0 -> 943 bytes
.../panda/resource/signednetwork/PN2.class | Bin 0 -> 1396 bytes
.../panda/resource/signednetwork/PN3.class | Bin 0 -> 1396 bytes
.../panda/resource/signednetwork/PN4.class | Bin 0 -> 2599 bytes
.../panda/resource/signednetwork/PN4C.class | Bin 0 -> 949 bytes
.../panda/resource/signednetwork/PP1.class | Bin 0 -> 3875 bytes
.../panda/resource/signednetwork/PP1C.class | Bin 0 -> 943 bytes
.../panda/resource/signednetwork/PP2.class | Bin 0 -> 2656 bytes
.../panda/resource/signednetwork/PP3.class | Bin 0 -> 2668 bytes
.../panda/resource/signednetwork/PP4.class | Bin 0 -> 4383 bytes
.../panda/resource/signednetwork/PP4C.class | Bin 0 -> 949 bytes
.../PhosphoInteractionCreator.class | Bin 0 -> 3759 bytes
.../signednetwork/SignedSIFInteraction.class | Bin 0 -> 3195 bytes
.../resource/signednetwork/SignedType.class | Bin 0 -> 4784 bytes
.../siteeffect/CustomSiteEffectServer.class | Bin 0 -> 2957 bytes
.../panda/resource/siteeffect/Feature.class | Bin 0 -> 1974 bytes
.../siteeffect/PhosphoSitePlus$1.class | Bin 0 -> 597 bytes
.../resource/siteeffect/PhosphoSitePlus.class | Bin 0 -> 8682 bytes
.../panda/resource/siteeffect/Signor$1.class | Bin 0 -> 531 bytes
.../panda/resource/siteeffect/Signor.class | Bin 0 -> 4918 bytes
.../siteeffect/SiteEffectCollective.class | Bin 0 -> 8805 bytes
.../siteeffect/SiteEffectServer.class | Bin 0 -> 9395 bytes
.../tcga/BroadDownloader$ResourceType.class | Bin 0 -> 1910 bytes
.../panda/resource/tcga/BroadDownloader.class | Bin 0 -> 8554 bytes
.../org/panda/resource/tcga/CNAReader.class | Bin 0 -> 8617 bytes
.../tcga/CustomExpressionReader.class | Bin 0 -> 2454 bytes
.../resource/tcga/ExpressionReader.class | Bin 0 -> 5929 bytes
.../panda/resource/tcga/MutSigReader.class | Bin 0 -> 2332 bytes
.../org/panda/resource/tcga/MutTuple.class | Bin 0 -> 746 bytes
.../panda/resource/tcga/MutationReader.class | Bin 0 -> 15118 bytes
.../tcga/ProteomicsFileRow$SiteEffect.class | Bin 0 -> 1766 bytes
.../tcga/ProteomicsFileRow$Type.class | Bin 0 -> 1424 bytes
.../resource/tcga/ProteomicsFileRow.class | Bin 0 -> 7765 bytes
.../org/panda/resource/tcga/RPPAReader.class | Bin 0 -> 9217 bytes
.../panda/resource/tcga/rppa-annotation.txt | 6 ++
119 files changed, 103 insertions(+), 1 deletion(-)
create mode 100644 resource.iml
create mode 100644 target/classes/org/panda/resource/CancerGeneBushman.class
create mode 100644 target/classes/org/panda/resource/CancerGeneCensus.class
create mode 100644 target/classes/org/panda/resource/ChEBI.class
create mode 100644 target/classes/org/panda/resource/Download.class
create mode 100644 target/classes/org/panda/resource/FileServer.class
create mode 100644 target/classes/org/panda/resource/GO.class
create mode 100644 target/classes/org/panda/resource/GWASCatalog.class
create mode 100644 target/classes/org/panda/resource/HG37.class
create mode 100644 target/classes/org/panda/resource/HGNC$1.class
create mode 100644 target/classes/org/panda/resource/HGNC.class
create mode 100644 target/classes/org/panda/resource/KinaseLibrary.class
create mode 100644 target/classes/org/panda/resource/MGI.class
create mode 100644 target/classes/org/panda/resource/MGIVertebrateHomology$Organism.class
create mode 100644 target/classes/org/panda/resource/MGIVertebrateHomology.class
create mode 100644 target/classes/org/panda/resource/MSigDB$NameFilter.class
create mode 100644 target/classes/org/panda/resource/MSigDB.class
create mode 100644 target/classes/org/panda/resource/MatrixOfValuesDatasetReader.class
create mode 100644 target/classes/org/panda/resource/OncoKB.class
create mode 100644 target/classes/org/panda/resource/PAM50.class
create mode 100644 target/classes/org/panda/resource/PCPathway.class
create mode 100644 target/classes/org/panda/resource/PCPathwayHGNC$Pathway.class
create mode 100644 target/classes/org/panda/resource/PCPathwayHGNC.class
create mode 100644 target/classes/org/panda/resource/PCPathwayUniprot.class
create mode 100644 target/classes/org/panda/resource/PiHelper.class
create mode 100644 target/classes/org/panda/resource/Pubmed.class
create mode 100644 target/classes/org/panda/resource/ReactomePathway.class
create mode 100644 target/classes/org/panda/resource/ResourceDirectory.class
create mode 100644 target/classes/org/panda/resource/SignedInteractionText.class
create mode 100644 target/classes/org/panda/resource/SiteMappingMouseToHuman.class
create mode 100644 target/classes/org/panda/resource/SiteMappingRatToHuman.class
create mode 100644 target/classes/org/panda/resource/UniProtSequence.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/DenovoDB$DataFilter.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/DenovoDB$DataFilterEnum.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/DenovoDB$Entry.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/DenovoDB.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/IossifovDataset$DataFilter.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/IossifovDataset$Entry.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/IossifovDataset.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/SFARI$Entry.class
create mode 100644 target/classes/org/panda/resource/autismdatasets/SFARI.class
create mode 100644 target/classes/org/panda/resource/network/ActivityNetwork.class
create mode 100644 target/classes/org/panda/resource/network/IPTMNet.class
create mode 100644 target/classes/org/panda/resource/network/NetworKIN.class
create mode 100644 target/classes/org/panda/resource/network/PathwayCommons.class
create mode 100644 target/classes/org/panda/resource/network/PhosphoNetworks.class
create mode 100644 target/classes/org/panda/resource/network/PhosphoSitePlus.class
create mode 100644 target/classes/org/panda/resource/network/RhoGEF.class
create mode 100644 target/classes/org/panda/resource/network/SignedMetabolic$1.class
create mode 100644 target/classes/org/panda/resource/network/SignedMetabolic.class
create mode 100644 target/classes/org/panda/resource/network/SignedPC.class
create mode 100644 target/classes/org/panda/resource/network/SignedPCNoTransfac.class
create mode 100644 target/classes/org/panda/resource/network/SignedREACH.class
create mode 100644 target/classes/org/panda/resource/network/TFactS.class
create mode 100644 target/classes/org/panda/resource/network/TRRUST.class
create mode 100644 target/classes/org/panda/resource/network/UniProt$Relation.class
create mode 100644 target/classes/org/panda/resource/network/UniProt$UPHandler.class
create mode 100644 target/classes/org/panda/resource/network/UniProt.class
create mode 100644 target/classes/org/panda/resource/proteomics/MDACCFormatRPPALoader.class
create mode 100644 target/classes/org/panda/resource/proteomics/RPPAIDMapper.class
create mode 100644 target/classes/org/panda/resource/signednetwork/ConflictResolver.class
create mode 100644 target/classes/org/panda/resource/signednetwork/ConflictResolverSimple.class
create mode 100644 target/classes/org/panda/resource/signednetwork/ControlSignConstraint$1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/ControlSignConstraint$Sign.class
create mode 100644 target/classes/org/panda/resource/signednetwork/ControlSignConstraint.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EN1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EN1C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EN2.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EN2C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EP1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EP1C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EP2.class
create mode 100644 target/classes/org/panda/resource/signednetwork/EP2C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/GN1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/GP1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/GTPChangeConstraint$Type.class
create mode 100644 target/classes/org/panda/resource/signednetwork/GTPChangeConstraint.class
create mode 100644 target/classes/org/panda/resource/signednetwork/Generator.class
create mode 100644 target/classes/org/panda/resource/signednetwork/InhibitionByBindingMiner$IsSubsetAndReverse.class
create mode 100644 target/classes/org/panda/resource/signednetwork/InhibitionByBindingMiner.class
create mode 100644 target/classes/org/panda/resource/signednetwork/Inhibits.class
create mode 100644 target/classes/org/panda/resource/signednetwork/NotLessDirect.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PN1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PN1C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PN2.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PN3.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PN4.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PN4C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PP1.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PP1C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PP2.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PP3.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PP4.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PP4C.class
create mode 100644 target/classes/org/panda/resource/signednetwork/PhosphoInteractionCreator.class
create mode 100644 target/classes/org/panda/resource/signednetwork/SignedSIFInteraction.class
create mode 100644 target/classes/org/panda/resource/signednetwork/SignedType.class
create mode 100644 target/classes/org/panda/resource/siteeffect/CustomSiteEffectServer.class
create mode 100644 target/classes/org/panda/resource/siteeffect/Feature.class
create mode 100644 target/classes/org/panda/resource/siteeffect/PhosphoSitePlus$1.class
create mode 100644 target/classes/org/panda/resource/siteeffect/PhosphoSitePlus.class
create mode 100644 target/classes/org/panda/resource/siteeffect/Signor$1.class
create mode 100644 target/classes/org/panda/resource/siteeffect/Signor.class
create mode 100644 target/classes/org/panda/resource/siteeffect/SiteEffectCollective.class
create mode 100644 target/classes/org/panda/resource/siteeffect/SiteEffectServer.class
create mode 100644 target/classes/org/panda/resource/tcga/BroadDownloader$ResourceType.class
create mode 100644 target/classes/org/panda/resource/tcga/BroadDownloader.class
create mode 100644 target/classes/org/panda/resource/tcga/CNAReader.class
create mode 100644 target/classes/org/panda/resource/tcga/CustomExpressionReader.class
create mode 100644 target/classes/org/panda/resource/tcga/ExpressionReader.class
create mode 100644 target/classes/org/panda/resource/tcga/MutSigReader.class
create mode 100644 target/classes/org/panda/resource/tcga/MutTuple.class
create mode 100644 target/classes/org/panda/resource/tcga/MutationReader.class
create mode 100644 target/classes/org/panda/resource/tcga/ProteomicsFileRow$SiteEffect.class
create mode 100644 target/classes/org/panda/resource/tcga/ProteomicsFileRow$Type.class
create mode 100644 target/classes/org/panda/resource/tcga/ProteomicsFileRow.class
create mode 100644 target/classes/org/panda/resource/tcga/RPPAReader.class
create mode 100644 target/classes/org/panda/resource/tcga/rppa-annotation.txt
diff --git a/resource.iml b/resource.iml
new file mode 100644
index 0000000..3f52f0d
--- /dev/null
+++ b/resource.iml
@@ -0,0 +1,56 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
\ No newline at end of file
diff --git a/src/main/java/org/panda/resource/UniProtSequence.java b/src/main/java/org/panda/resource/UniProtSequence.java
index 726d172..f3a5266 100644
--- a/src/main/java/org/panda/resource/UniProtSequence.java
+++ b/src/main/java/org/panda/resource/UniProtSequence.java
@@ -5,6 +5,7 @@
package org.panda.resource;
+
import java.io.BufferedReader;
import java.io.IOException;
import java.util.HashMap;
@@ -129,6 +130,19 @@ public String getSeqAround(String idOrName, int prefixLen, int suffixLen, int lo
*/
int max = ((prefixLen > suffixLen ? prefixLen : suffixLen) * 2) + 1;
+
+
+// max/2 is how many you want to left/right of central position
+ // if you want k to the right, and you are at the kth position or lesser, this is impossible
+ if(max/2 >= location){
+ return null;
+ }
+
+ /*
+ The call to getSeqAround takes the width as an argument. Consider, if the width/2 = k,
+ then there will be k amino acids to the left and to the right.
+ */
+
// Will take an odd-length as argument, and return sequence of that length
// centered around location
@@ -189,7 +203,31 @@ public boolean load() throws IOException {
this.nameToID.put(name, id);
sequence = new StringBuilder();
int oInd = line.indexOf(" OX=");
- String organism = line.substring(oInd + 4, line.indexOf(" ", oInd + 4));
+
+ /*
+ System.out.println("\n New line of printing");
+ System.out.println(oInd);
+ System.out.println(line);
+
+ */
+
+ /*
+ What is the issue here?
+ */
+
+ /*
+ if(line.indexOf(" ", oInd + 4) <= -1){
+ System.out.println(line);
+ continue;
+ }
+
+ */
+
+ String organism = line. substring(oInd + 4, line.indexOf(" ", oInd + 4));
+
+ // System.out.println(organism);
+ // System.out.println("");
+
int sInd = line.indexOf(" GN=");
if (sInd > 0) {
String symbol = line.substring(sInd + 4, line.indexOf(" ", sInd + 4));
@@ -202,9 +240,11 @@ public boolean load() throws IOException {
}
} else {
sequence.append(line);
+
}
}
+
reader.close();
return true;
}
diff --git a/target/classes/org/panda/resource/CancerGeneBushman.class b/target/classes/org/panda/resource/CancerGeneBushman.class
new file mode 100644
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