JAL-2629 buffers are now temporary files

diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
index 3879a87..79a8092 100644 (file)
--- a/src/jalview/hmmer/HMMAlignThread.java
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -1,17 +1,19 @@
 package jalview.hmmer;
 
 import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentOrder;
 import jalview.datamodel.HiddenMarkovModel;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.io.FileLoader;
 import jalview.util.MessageManager;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.HashMap;
@@ -19,6 +21,7 @@ import java.util.Map;
 
 public class HMMAlignThread implements Runnable
 {
+  HMMERCommands cmds = new HMMERCommands();
 
   AlignFrame af;
 
@@ -46,13 +49,28 @@ public class HMMAlignThread implements Runnable
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             barID);
-    HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+    cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+    try
+    {
+      cmds.HMMBUFFER = File.createTempFile("hmm", ".hmm").getAbsolutePath()
+              + cmds.SPACE;
+      cmds.ALIGNMENTBUFFER = File.createTempFile("output", ".sto")
+              .getAbsolutePath() + cmds.SPACE;
+      cmds.ALIGNMENTINPUT = File.createTempFile("input", ".sto")
+              .getAbsolutePath() + cmds.SPACE;
+      cmds.OUTPUTALIGNMENT = "-o " + cmds.ALIGNMENTINPUT + cmds.SPACE;
+    } catch (IOException e1)
+    {
+      // TODO Auto-generated catch block
+      e1.printStackTrace();
+    }
+
     try
     {
       try
       {
         hmmSeqs = alignment.getHMMConsensusSequences(true);
-        HMMERCommands.exportData(alignment, true, true, hmm);
+        cmds.exportData(alignment, true, true, hmm);
       } catch (FileNotFoundException e)
       {
         // TODO Auto-generated catch block
@@ -87,16 +105,14 @@ public class HMMAlignThread implements Runnable
 
   private void runCommand() throws IOException, InterruptedException
   {
-    String command = HMMERCommands.HMMERFOLDER + HMMERCommands.HMMALIGN;
+    String command = cmds.HMMERFOLDER + cmds.HMMALIGN;
     if (!hmm.getFileHeader().contains("HMMER3/f"))
     {
-      command += HMMERCommands.ALLCOL;
+      command += cmds.ALLCOL;
     }
-    command += HMMERCommands.TRIM + HMMERCommands.OUTPUTALIGNMENT
-            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
-            + HMMERCommands.JALVIEWDIRECTORY
-            + HMMERCommands.ALIGNMENTBUFFER;
-    HMMERCommands.runCommand(command);
+    command += cmds.TRIM + cmds.OUTPUTALIGNMENT + cmds.HMMBUFFER
+            + cmds.ALIGNMENTBUFFER;
+    cmds.runCommand(command);
   }
 
   private void importData() throws IOException, InterruptedException
@@ -104,22 +120,32 @@ public class HMMAlignThread implements Runnable
     if (newFrame)
     {
       FileLoader loader = new FileLoader();
-      AlignmentOrder order = new AlignmentOrder(alignment);
-      AlignFrame newAFrame = loader.LoadFileWaitTillLoaded(
-              HMMERCommands.ALIGNMENTINPUT, DataSourceType.FILE);
+      AlignFrame aFrame = new AlignFrame(new Alignment(new SequenceI[1]),
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      Desktop.addInternalFrame(aFrame, aFrame.getTitle(),
+              AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+      aFrame.setTitle(
+              af.getName() + "Aligned to " + hmm.getName() + "'s HMM");
+      af.getViewport().setAlignment(null);
+
+      aFrame.loadJalviewDataFile(cmds.ALIGNMENTINPUT,
+              DataSourceType.FILE, FileFormat.Stockholm, null);
+
+
+
       Map<Integer, SequenceI> copy = new HashMap<>(
               hmmSeqs);
-      addSeqs(newAFrame, copy);
-      SequenceI seq = newAFrame.getViewport().getAlignment()
+      addSeqs(aFrame, copy);
+      SequenceI seq = aFrame.getViewport().getAlignment()
               .getSequenceAt(0);
-      hmm.mapToReferenceAnnotation(newAFrame, seq);
+      seq.getHMM().mapToReferenceAnnotation(aFrame, seq);
       addSeqs(af, hmmSeqs);
     }
     else
     {
       af.getViewport().getAlignment().getSequences().clear();
       af.setIsRecurring(true);
-      af.loadJalviewDataFile(HMMERCommands.ALIGNMENTBUFFER,
+      af.loadJalviewDataFile(cmds.ALIGNMENTBUFFER,
               DataSourceType.FILE, FileFormat.Stockholm, null);
       af.setIsRecurring(false);
       addSeqs(af, hmmSeqs);
@@ -132,7 +158,7 @@ public class HMMAlignThread implements Runnable
     {
       SequenceI seq = entry.getValue();
       Integer pos = entry.getKey();
-      HMMERCommands.addHMMConsensusSequence(alignFrame, seq, pos);
+      cmds.addHMMConsensusSequence(alignFrame, seq, pos);
     }
   }
 

diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index e48dce3..cf89863 100644 (file)
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -10,13 +10,14 @@ import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
 import jalview.util.MessageManager;
 
+import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.util.Map;
 
 public class HMMBuildThread implements Runnable
 {
-
+  HMMERCommands cmds = new HMMERCommands();
   AlignFrame af;
   AlignmentI alignment;
 
@@ -36,14 +37,24 @@ public class HMMBuildThread implements Runnable
     barID = System.currentTimeMillis();
     af.setProgressBar(MessageManager.getString("status.running_hmmbuild"),
             barID);
-    HMMERCommands.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+    cmds.HMMERFOLDER = Cache.getProperty(Preferences.HMMER_PATH);
+    try
+    {
+      cmds.HMMBUFFER = File.createTempFile("hmm", ".hmm").getAbsolutePath()
+              + cmds.SPACE;
+      cmds.ALIGNMENTBUFFER = File.createTempFile("output", ".sto")
+              .getAbsolutePath() + cmds.SPACE;
+    } catch (IOException e1)
+    {
+      e1.printStackTrace();
+    }
 
     try
     {
     try
     {
         hmmSeqs = alignment.getHMMConsensusSequences(true);
-        HMMERCommands.exportData(alignment, true, false,
+        cmds.exportData(alignment, true, false,
                 new HiddenMarkovModel());
     } catch (FileNotFoundException e)
     {
@@ -82,23 +93,21 @@ public class HMMBuildThread implements Runnable
   
   private void runCommand() throws IOException, InterruptedException
   {
-    final String command = HMMERCommands.HMMERFOLDER
-            + HMMERCommands.HMMBUILD + HMMERCommands.NAME
-            + af.getName() + HMMERCommands.SPACE
-            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.HMMBUFFER
-            + HMMERCommands.JALVIEWDIRECTORY + HMMERCommands.ALIGNMENTBUFFER;
-    HMMERCommands.runCommand(command);
+    final String command = cmds.HMMERFOLDER + cmds.HMMBUILD + cmds.NAME
+            + af.getName() + cmds.SPACE + cmds.HMMBUFFER
+            + cmds.ALIGNMENTBUFFER;
+    cmds.runCommand(command);
   }
   
   private void importData() throws IOException, InterruptedException
   {
-    af.loadJalviewDataFile(HMMERCommands.HMMBUFFER, DataSourceType.FILE,
+    af.loadJalviewDataFile(cmds.HMMBUFFER, DataSourceType.FILE,
             FileFormat.HMMER3, null);
     for (Map.Entry<Integer, SequenceI> entry : hmmSeqs.entrySet())
     {
       SequenceI seq = entry.getValue();
       Integer pos = entry.getKey();
-      HMMERCommands.addHMMConsensusSequence(af, seq, pos);
+      cmds.addHMMConsensusSequence(af, seq, pos);
     }
     af.alignPanel.alignmentChanged();
   }

diff --git a/src/jalview/hmmer/HMMERCommands.java b/src/jalview/hmmer/HMMERCommands.java
index 54516b5..5e35ef0 100644 (file)
--- a/src/jalview/hmmer/HMMERCommands.java
+++ b/src/jalview/hmmer/HMMERCommands.java
@@ -17,33 +17,32 @@ import java.util.List;
 public class HMMERCommands
 {
   // Path of hmmer binaries directory
-  static String HMMERFOLDER = "/Documents/";
+  String HMMERFOLDER = "/Documents/";
 
-  static final String JALVIEWDIRECTORY = System.getProperty("user.dir")
+  public String JALVIEWDIRECTORY = System.getProperty("user.dir")
           + "/";
 
-  static String HMMALIGN = "/hmmalign ";
+  public String HMMALIGN = "/hmmalign ";
 
-  static String HMMBUILD = "/hmmbuild ";
+  public String HMMBUILD = "/hmmbuild ";
 
-  static String HMMSEARCH = "/hmmsearch ";
+  public String HMMSEARCH = "/hmmsearch ";
 
-  static final String HMMBUFFER = "src/jalview/hmmer/hmm_buffer.hmm ";
+  public String HMMBUFFER;
 
-  static final String ALIGNMENTBUFFER = "src/jalview/hmmer/alignment_buffer.sto ";
+  public String ALIGNMENTBUFFER;
 
-  static final String ALIGNMENTINPUT = "src/jalview/hmmer/alignment_input.sto ";
+  public String ALIGNMENTINPUT;
 
-  static final String OUTPUTALIGNMENT = "-o " + JALVIEWDIRECTORY
-          + ALIGNMENTINPUT;
+  public String OUTPUTALIGNMENT;
 
-  static final String NAME = "-n ";
+  public String NAME = "-n ";
 
-  static final String SPACE = " ";
+  public String SPACE = " ";
 
-  static final String ALLCOL = "--allcol ";
+  public String ALLCOL = "--allcol ";
 
-  static final String TRIM = "--trim ";
+  public String TRIM = "--trim ";
 
 
   /**
@@ -53,7 +52,7 @@ public class HMMERCommands
    * @throws IOException
    * @throws InterruptedException
    */
-  public static void runCommand(String command)
+  public void runCommand(String command)
           throws IOException, InterruptedException
   {
     final Process p = Runtime.getRuntime().exec(command);
@@ -89,7 +88,7 @@ public class HMMERCommands
    * @param alignment
    * @throws IOException
    */
-  public static void exportData(AlignmentI alignment,
+  public void exportData(AlignmentI alignment,
           boolean exportAlignment, boolean exportHMM, HiddenMarkovModel hmm)
           throws IOException
   {
@@ -117,7 +116,7 @@ public class HMMERCommands
     }
   }
 
-  public static void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
+  public void addHMMConsensusSequence(AlignFrame af, SequenceI seq,
           Integer position)
   {
     seq.getHMM().initHMMSequence(af, position);