change parameter file name

cctsou · Jan 9, 2016 · 993cd22 · 993cd22
1 parent 9d064e7
commit 993cd22
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Showing 11 changed files with 14 additions and 11 deletions.
diff --git a/CrossLinker/nbproject/private/private.xml b/CrossLinker/nbproject/private/private.xml
@@ -33,14 +33,14 @@
             <file>file:/C:/Umich/MS-Umpire/CrossLinker/src/crosslinker/CrossLinkerHandler.java</file>
         </group>
         <group name="DIA-Umpire_Release">
-            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CXL_MALDI.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java</file>
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CrosslinkerPepFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/CXL_MALDI.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PeakPairFinder.java</file>
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/MS2PeakPairFinder.java</file>
+            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/Exec/cxl.params</file>
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/SortedFragFinder.java</file>
             <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/Exec/CrossLinkerDetection.java</file>
-            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/Exec/cxl.params</file>
-            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PeakPairFinder.java</file>
-            <file>file:/C:/Umich/GitHub/DIA-Umpire/CrossLinker/src/CXL_PeakPairFinder/PrecursorCrossPepFinder.java</file>
         </group>
     </open-files>
 </project-private>
diff --git a/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCurve.java b/DIA-Umpire/src/MSUmpire/PeakDataStructure/PeakCurve.java
@@ -40,6 +40,9 @@ public class PeakCurve implements Serializable  {
     //Y: m/z
     //Z: intensity
     private XYPointCollection SmoothData;
+    //X: retention time
+    //Y: intensity
+    //XIC
     private float startint = 0f;
     public int Index;
     private float endrt = -1f;

diff --git a/DIA_Umpire_ExtLibSearch/src/dia_umpire_quant/DIA_Umpire_ExtLibSearch.java b/DIA_Umpire_ExtLibSearch/src/dia_umpire_quant/DIA_Umpire_ExtLibSearch.java
@@ -56,7 +56,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         System.out.println("=================================================================================================");
         System.out.println("DIA-Umpire targeted re-extraction analysis using external library (version: " + UmpireInfo.GetInstance().Version + ")");
         if (args.length != 1) {
-            System.out.println("command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire.module_params");
+            System.out.println("command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_ExtLibSearch.jar diaumpire_module.params");
             return;
         }
         try {

diff --git a/DIA_Umpire_IntLibSearch/src/dia_umpire_quant/DIA_Umpire_IntLibSearch.java b/DIA_Umpire_IntLibSearch/src/dia_umpire_quant/DIA_Umpire_IntLibSearch.java
@@ -58,7 +58,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         System.out.println("=================================================================================================");
         System.out.println("DIA-Umpire targeted re-extraction analysis using internal library (version: " + UmpireInfo.GetInstance().Version + ")");
         if (args.length != 1) {
-            System.out.println("command format error, the correct format should be : java -jar -Xmx10G DIA_Umpire_IntLibSearch.jar diaumpire.module_params");
+            System.out.println("command format error, the correct format should be : java -jar -Xmx10G DIA_Umpire_IntLibSearch.jar diaumpire_module.params");
             return;
         }
         try {

diff --git a/DIA_Umpire_LCMSIDGen/src/dia_umpire_quant/DIA_Umpire_LCMSIDGen.java b/DIA_Umpire_LCMSIDGen/src/dia_umpire_quant/DIA_Umpire_LCMSIDGen.java
@@ -50,7 +50,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         System.out.println("=================================================================================================");
         System.out.println("DIA-Umpire LCMSID geneartor (version: " + UmpireInfo.GetInstance().Version + ")");
         if (args.length != 1) {
-            System.out.println("command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire.module_params");
+            System.out.println("command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_LCMSIDGen.jar diaumpire_module.params");
             return;
         }
         try {

diff --git a/DIA_Umpire_ProtQuant/src/dia_umpire_quant/DIA_Umpire_ProtQuant.java b/DIA_Umpire_ProtQuant/src/dia_umpire_quant/DIA_Umpire_ProtQuant.java
@@ -63,7 +63,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         System.out.println("=================================================================================================");
         System.out.println("DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")");
         if (args.length != 1) {
-            System.out.println("command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire.module_params");
+            System.out.println("command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params");
             return;
         }
         try {

diff --git a/DIA_Umpire_Quant/src/dia_umpire_quant/DIA_Umpire_Quant.java b/DIA_Umpire_Quant/src/dia_umpire_quant/DIA_Umpire_Quant.java
@@ -71,7 +71,7 @@ public static void main(String[] args) throws FileNotFoundException, IOException
         System.out.println("=================================================================================================");
         System.out.println("DIA-Umpire quantitation with targeted re-extraction analysis (version: " + UmpireInfo.GetInstance().Version + ")");
         if (args.length != 1) {
-            System.out.println("command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire.quant_params");
+            System.out.println("command format error, it should be like: java -jar -Xmx10G DIA_Umpire_Quant.jar diaumpire_quant.params");
             return;
         }
         try {

diff --git a/.../dia_umpire_quant/diaumpire.module_params → .../dia_umpire_quant/diaumpire_module.params b/.../dia_umpire_quant/diaumpire.module_params → .../dia_umpire_quant/diaumpire_module.params
diff --git a/...c/dia_umpire_quant/diaumpire.quant_params → ...c/dia_umpire_quant/diaumpire_quant.params b/...c/dia_umpire_quant/diaumpire.quant_params → ...c/dia_umpire_quant/diaumpire_quant.params
diff --git a/DIA_Umpire_SE/src/dia_umpire_se/DIA_Umpire_SE.java b/DIA_Umpire_SE/src/dia_umpire_se/DIA_Umpire_SE.java
@@ -54,8 +54,8 @@ public static void main(String[] args) throws InterruptedException, FileNotFound
         System.out.println("=================================================================================================");
         System.out.println("DIA-Umpire singal extraction analysis  (version: " + UmpireInfo.GetInstance().Version + ")");
         if (args.length < 2 || args.length > 3) {
-            System.out.println("command format error, the correct format is: java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire.se_params");
-            System.out.println("To fix DIA setting, use : java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire.se_params -f");
+            System.out.println("command format error, the correct format is: java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire_se.params");
+            System.out.println("To fix DIA setting, use : java -jar -Xmx8G DIA_Umpire_SE.jar mzMXL_file diaumpire_se.params -f");
             return;
         }
         try {

diff --git a/..._SE/src/dia_umpire_se/diaumpire.se_params → ..._SE/src/dia_umpire_se/diaumpire_se.params b/..._SE/src/dia_umpire_se/diaumpire.se_params → ..._SE/src/dia_umpire_se/diaumpire_se.params