Code cleanup - generics and warnings (#924)

Author: labkey-jeckels

ms2/src/org/labkey/ms2/PeptideProphetGraphs.java

@@ -182,7 +182,7 @@ public static void renderObservedVsPPScore(HttpServletResponse response, Contain
 
             if (count == increment)
             {
-                negative += negative * ratioRandom; // add back random positives
+                negative += (int)(negative * ratioRandom); // add back random positives
                 if (negative > count)
                     negative = count;
                 score /= (float) count; // mean score

ms2/src/org/labkey/ms2/pipeline/FastaCheckTask.java

@@ -55,7 +55,7 @@ public Factory()
         }
 
         @Override
-        public PipelineJob.Task createTask(PipelineJob job)
+        public FastaCheckTask createTask(PipelineJob job)
         {
             return new FastaCheckTask(this, job);
         }

ms2/src/org/labkey/ms2/pipeline/comet/CometSearchProtocol.java

@@ -19,7 +19,6 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineValidationException;
-import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;
 import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol;
@@ -42,7 +41,7 @@ public CometSearchProtocol(String name, String description, String xml, Containe
     }
 
     @Override
-    public AbstractFileAnalysisProtocolFactory getFactory()
+    public CometSearchProtocolFactory getFactory()
     {
         return CometSearchProtocolFactory.get();
     }

ms2/src/org/labkey/ms2/pipeline/mascot/MascotSearchProtocol.java

@@ -18,7 +18,6 @@
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipeRoot;
-import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol;
 
@@ -39,7 +38,7 @@ public MascotSearchProtocol(String name, String description, String xml, Contain
     }
 
     @Override
-    public AbstractFileAnalysisProtocolFactory getFactory()
+    public MascotSearchProtocolFactory getFactory()
     {
         return MascotSearchProtocolFactory.get();
     }

ms2/src/org/labkey/ms2/pipeline/sequest/SequestSearchProtocol.java

@@ -20,7 +20,7 @@
 import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipeRoot;
 import org.labkey.api.pipeline.PipelineValidationException;
-import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol;
 
@@ -43,7 +43,7 @@ public SequestSearchProtocol(String name, String description, String xml, Contai
     }
 
     @Override
-    public AbstractFileAnalysisProtocolFactory getFactory()
+    public SequestSearchProtocolFactory getFactory()
     {
         return SequestSearchProtocolFactory.get();
     }
@@ -65,7 +65,7 @@ public void validate(PipeRoot root) throws PipelineValidationException
         if(dbNames.isEmpty())
             throw new IllegalArgumentException("A sequence database must be selected.");
 
-        File fileSequenceDB = new File(getDirSeqRoot(), dbNames.get(0));
+        File fileSequenceDB = FileUtil.appendPath(getDirSeqRoot(), org.labkey.api.util.Path.parse(dbNames.get(0)));
         if (!fileSequenceDB.exists())
             throw new IllegalArgumentException("Sequence database '" + dbNames.get(0) + "' is not found in local FASTA root.");
 

ms2/src/org/labkey/ms2/pipeline/tandem/XTandemSearchProtocol.java

@@ -15,12 +15,9 @@
  */
 package org.labkey.ms2.pipeline.tandem;
 
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.data.Container;
 import org.labkey.api.pipeline.PipeRoot;
-import org.labkey.api.pipeline.file.AbstractFileAnalysisProtocolFactory;
 import org.labkey.api.view.ViewBackgroundInfo;
 import org.labkey.ms2.pipeline.AbstractMS2SearchProtocol;
 
@@ -38,15 +35,13 @@
  */
 public class XTandemSearchProtocol extends AbstractMS2SearchProtocol<XTandemPipelineJob>
 {
-    private static final Logger _log = LogManager.getLogger(XTandemSearchProtocol.class);
-
     public XTandemSearchProtocol(String name, String description, String xml, Container container)
     {
         super(name, description, xml, container);
     }
 
     @Override
-    public AbstractFileAnalysisProtocolFactory getFactory()
+    public XTandemSearchProtocolFactory getFactory()
     {
         return XTandemSearchProtocolFactory.get();
     }

ms2/src/org/labkey/ms2/reader/MascotDatLoader.java

@@ -149,7 +149,7 @@ public class MascotDatLoader extends MS2Loader implements AutoCloseable
     // once URL decoded, the value looks like this:
     //  CAexample_mini.0110.0110.1
 
-    public static final Pattern QUERY_TITLE_SCAN_REGEX = Pattern.compile("\\.??(\\d{1,6})\\.(\\d{1,6})\\.(\\d)\\.??[a-zA-z0-9_]*?$");
+    public static final Pattern QUERY_TITLE_SCAN_REGEX = Pattern.compile("\\.??(\\d{1,6})\\.(\\d{1,6})\\.(\\d)\\.??[a-zA-Z0-9_]*?$");
     // the title line may also look like this:
     // title=Spectrum270258%20scans%3a6721%2c
     // decoded to: