From 0130de04e06f678a8d914bc5acb030eb19e6d334 Mon Sep 17 00:00:00 2001 From: Chih-Chiang Tsou Date: Fri, 20 Nov 2015 23:34:05 -0500 Subject: [PATCH] v1.4273 --- .../MSUmpire/PSMDataStructure/PTMManager.java | 2 +- .../MSUmpire/PSMDataStructure/PepIonID.java | 2 +- .../src/MSUmpire/PSMDataStructure/ProtID.java | 2 +- .../ProtXMLParseHandler.java | 23 +++++++++++++++---- .../src/dia_umpire_to_skyline/FileThread.java | 2 +- 5 files changed, 23 insertions(+), 8 deletions(-) diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PTMManager.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PTMManager.java index dc535bf..5c7e029 100644 --- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PTMManager.java +++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PTMManager.java @@ -123,7 +123,7 @@ public PTM GetPTM(String AA, float massdiff) { } if (sitecorrect) { double diff = Math.abs(ptm.getMass() - massdiff); - if (diff < 1f) { + if (diff < 0.5f) { if (diff < smallmassdiff) { smallmassdiff = diff; smallestdiffptm = ptm; diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java index d6290a2..3f8b1ef 100644 --- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java +++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/PepIonID.java @@ -269,7 +269,7 @@ public boolean IsDecoy(String decoytag) { if (IsDecoy == -1) { IsDecoy = 1; for (String pro : ParentProtID_PepXML) { - if (!pro.startsWith(decoytag)) { + if (!(pro.startsWith(decoytag) | pro.endsWith(decoytag))) { IsDecoy = 0; break; } diff --git a/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java b/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java index 0071a9c..3bc9336 100644 --- a/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java +++ b/DIA-Umpire/src/MSUmpire/PSMDataStructure/ProtID.java @@ -238,7 +238,7 @@ public String GetGeneName() { } public boolean IsDecoy(String decoytag) { - if (getAccNo().startsWith(decoytag)) { + if (getAccNo().startsWith(decoytag) | getAccNo().endsWith(decoytag)) { return true; } return false; diff --git a/DIA-Umpire/src/MSUmpire/SearchResultParser/ProtXMLParseHandler.java b/DIA-Umpire/src/MSUmpire/SearchResultParser/ProtXMLParseHandler.java index 9570b86..afb034c 100644 --- a/DIA-Umpire/src/MSUmpire/SearchResultParser/ProtXMLParseHandler.java +++ b/DIA-Umpire/src/MSUmpire/SearchResultParser/ProtXMLParseHandler.java @@ -57,7 +57,15 @@ public void handle(Element node) throws Exception { private void ParseProteinGroupNode(Element protgroupnode) throws XmlPullParserException, IOException, ClassNotFoundException, InterruptedException { int groupindex = Integer.parseInt(protgroupnode.getAttributes().getNamedItem("group_number").getNodeValue()); - float groupprob = Float.parseFloat(protgroupnode.getAttributes().getNamedItem("probability").getNodeValue()); + + float groupprob=0f; + if (protgroupnode.getAttributes().getNamedItem("probability") != null) { + groupprob = Float.parseFloat(protgroupnode.getAttributes().getNamedItem("probability").getNodeValue()); + } + else if (protgroupnode.getAttributes().getNamedItem("probability") != null) { + groupprob = Float.parseFloat(protgroupnode.getAttributes().getNamedItem("group_probability").getNodeValue()); + } + int alphabet = 1; for (int j = 0; j < protgroupnode.getChildNodes().getLength(); j++) { @@ -154,9 +162,16 @@ private void ParseProteinGroupNode(Element protgroupnode) throws XmlPullParserEx } else { PepIonID pepIonID = new PepIonID(); pepIonID.Sequence = child.getAttributes().getNamedItem("peptide_sequence").getNodeValue(); - pepIonID.MaxProbability = Float.parseFloat(child.getAttributes().getNamedItem("initial_probability").getNodeValue()); - pepIonID.Is_NonDegenerate = "Y".equals(child.getAttributes().getNamedItem("is_nondegenerate_evidence").getNodeValue()); - pepIonID.Weight = Float.parseFloat(child.getAttributes().getNamedItem("weight").getNodeValue()); + + if (child.getAttributes().getNamedItem("initial_probability") != null) { + pepIonID.MaxProbability = Float.parseFloat(child.getAttributes().getNamedItem("initial_probability").getNodeValue()); + } + if (child.getAttributes().getNamedItem("is_nondegenerate_evidence") != null) { + pepIonID.Is_NonDegenerate = "Y".equals(child.getAttributes().getNamedItem("is_nondegenerate_evidence").getNodeValue()); + } + if (child.getAttributes().getNamedItem("weight") != null) { + pepIonID.Weight = Float.parseFloat(child.getAttributes().getNamedItem("weight").getNodeValue()); + } if (child.getAttributes().getNamedItem("group_weight") != null) { pepIonID.GroupWeight = Float.parseFloat(child.getAttributes().getNamedItem("group_weight").getNodeValue()); } diff --git a/DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java b/DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java index 15b5386..c47d052 100644 --- a/DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java +++ b/DIA_Umpire_To_Skyline/src/dia_umpire_to_skyline/FileThread.java @@ -110,7 +110,7 @@ private void ChangeScanTitlePepXML() throws FileNotFoundException, IOException{ writer.write(line.replaceAll(basename+"_Q",basename+".ForLibQ")+"\n"); } writer.close(); - } + } } } }