From: tzvanaalten <tzvanaalten@172.17.105.62>
Date: Tue, 15 Aug 2017 15:18:58 +0000 (+0100)
Subject: JAL-2629 fix file loading issues on Mac
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=d1f25a5bd328b4f9a47bf98fe85e00209b91e0f2

JAL-2629 fix file loading issues on Mac
---

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 0e418bd..7a231bc 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -694,8 +694,8 @@ public class Preferences extends GPreferences
     }
     if (hmmerStatus)
     {
-      String ver = getHMMERVersion();
-      Cache.setProperty("HMMER_VERSION", ver);
+      // String ver = getHMMERVersion();
+      Cache.setProperty("HMMER_VERSION", "3.1b2");
     }
     
     
@@ -1209,7 +1209,7 @@ public class Preferences extends GPreferences
         return false;
       }
 
-      File hmmbuild = new File(path + "/binaries/hmmbuild.exe");
+      File hmmbuild = new File(path + "/binaries/hmmbuild");
       {
         if (!hmmbuild.canExecute())
         {
@@ -1219,7 +1219,7 @@ public class Preferences extends GPreferences
         }
       }
 
-      File hmmalign = new File(path + "/binaries/hmmalign.exe");
+      File hmmalign = new File(path + "/binaries/hmmalign");
       {
         if (!hmmalign.canExecute())
         {
@@ -1229,7 +1229,7 @@ public class Preferences extends GPreferences
         }
       }
 
-      File hmmsearch = new File(path + "/binaries/hmmsearch.exe");
+      File hmmsearch = new File(path + "/binaries/hmmsearch");
       {
         if (!hmmsearch.canExecute())
         {
@@ -1271,7 +1271,7 @@ public class Preferences extends GPreferences
 
   private String getHMMERVersion()
   {
-    File file = new File(hmmerPath.getText() + "/release-notes.txt");
+    File file = new File(hmmerPath.getText() + "/release-notes");
     Scanner scanner = null;
     try
     {
diff --git a/src/jalview/hmmer/HMMAlignThread.java b/src/jalview/hmmer/HMMAlignThread.java
index 3649108..303b58b 100644
--- a/src/jalview/hmmer/HMMAlignThread.java
+++ b/src/jalview/hmmer/HMMAlignThread.java
@@ -165,7 +165,7 @@ public class HMMAlignThread implements Runnable
 
   private boolean runCommand() throws IOException, InterruptedException
   {
-    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmalign.exe");
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmalign");
     if (!file.canExecute())
     {
       return false;
diff --git a/src/jalview/hmmer/HMMBuildThread.java b/src/jalview/hmmer/HMMBuildThread.java
index 853b5f1..5d55f84 100644
--- a/src/jalview/hmmer/HMMBuildThread.java
+++ b/src/jalview/hmmer/HMMBuildThread.java
@@ -10,6 +10,7 @@ import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
+import jalview.io.FileLoader;
 import jalview.util.MessageManager;
 
 import java.io.File;
@@ -148,7 +149,7 @@ public class HMMBuildThread implements Runnable
   
   private boolean runCommand() throws IOException, InterruptedException
   {
-    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild.exe");
+    File file = new File(cmds.HMMERFOLDER + "/binaries/hmmbuild");
     if (!file.canExecute())
     {
       return false;
@@ -185,8 +186,10 @@ public class HMMBuildThread implements Runnable
   private void importData() throws IOException, InterruptedException
   {
     cmds.addHMMConsensusSequences(af);
-    af.loadJalviewDataFile(hmmTemp.getAbsolutePath(), DataSourceType.FILE,
-            FileFormat.HMMER3, null);
+    FileLoader loader = new FileLoader();
+    loader.LoadFileOntoAlignmentWaitTillLoaded(af.getViewport(),
+            hmmTemp.getAbsolutePath(), DataSourceType.FILE,
+            FileFormat.HMMER3);
     hmmTemp.delete();
     stoTemp.delete();
   }
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f04b88d..088e384 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -29,6 +29,8 @@ import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
+import jalview.datamodel.Profile;
+import jalview.datamodel.Profiles;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -200,6 +202,32 @@ public class FileLoader implements Runnable
     return alignFrame;
   }
 
+  public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
+          String file, DataSourceType sourceType, FileFormatI format)
+  {
+    this.viewport = viewport;
+    this.file = file;
+    this.protocol = sourceType;
+    this.format = format;
+    _LoadAlignmentFileWaitTillLoaded();
+  }
+
+  protected void _LoadAlignmentFileWaitTillLoaded()
+  {
+    Thread loader = new Thread(this);
+    loader.start();
+
+    while (loader.isAlive())
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (Exception ex)
+      {
+      }
+    }
+  }
+
   public void updateRecentlyOpened()
   {
     Vector recent = new Vector();
@@ -413,17 +441,11 @@ public class FileLoader implements Runnable
               }
               else
               {
-                  for (int i = 0; i < alignment.getAbsoluteHeight(); i++)
-                  {
-                    if (!alignment.getSequenceAt(i).isHMMConsensusSequence())
-                    {
-                      alignment.getSequences().add(i, seq);
-                      break;
-                    }
-                }
+                alignment.insertSequenceAt(0, seq);
               }
-              viewport.setAlignment(alignment);
               viewport.initInformation();
+              viewport.setSequenceInformationHash(
+                      new Profiles(new Profile[1]), 0);
               viewport.updateInformation(viewport.getAlignPanel());
               viewport.getAlignPanel().adjustAnnotationHeight();
               viewport.updateSequenceIdColours();
@@ -433,10 +455,8 @@ public class FileLoader implements Runnable
                 viewport.getAlignPanel().alignFrame
                         .setSelectedHMM(seq.getHMM());
               }
-              viewport.getAlignPanel().repaint();
               viewport.alignmentChanged(viewport.getAlignPanel());
 
-
             }
           }
           else