X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fvarna%2FVarnaCommands.java;h=f2a2b639a78055d96cd52a137da3db9d943b43f3;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=b5f0dc923e24a93ab898cb9f864ef2f9e39c3bc0;hpb=8d2724b83aca38ef75d68787cc5939d950467e63;p=jalview.git

diff --git a/src/jalview/ext/varna/VarnaCommands.java b/src/jalview/ext/varna/VarnaCommands.java
index b5f0dc9..f2a2b63 100644
--- a/src/jalview/ext/varna/VarnaCommands.java
+++ b/src/jalview/ext/varna/VarnaCommands.java
@@ -1,170 +1,170 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.ext.varna;
-
-import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
-
-import java.awt.Color;
-import java.util.ArrayList;
-
-/**
+ */
+package jalview.ext.varna;
+
+import jalview.api.FeatureRenderer;
+import jalview.api.SequenceRenderer;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Color;
+import java.util.ArrayList;
+
+/**
  * Routines for generating Jmol commands for Jalview/Jmol binding another
  * cruisecontrol test.
- * 
- * @author JimP
- *
- */
-public class VarnaCommands
-{
-
-  /**
+ * 
+ * @author JimP
+ * 
+ */
+public class VarnaCommands
+{
+
+  /**
    * Jmol utility which constructs the commands to colour chains by the given
    * alignment
-   * 
-   */
+   * 
+   */
   public static String[] getColourBySequenceCommand(
           StructureSelectionManager ssm, String[] files,
           SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
           AlignmentI alignment)
-  {
-	
-    ArrayList<String> str = new ArrayList<String>();
-    StringBuffer command = new StringBuffer();
-  
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
-    {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-  
-      if (mapping == null || mapping.length < 1)
-        continue;
-  
-      int lastPos = -1;
-      for (int s = 0; s < sequence[pdbfnum].length; s++)
-      {
-        for (int sp, m = 0; m < mapping.length; m++)
-        {
-          if (mapping[m].getSequence() == sequence[pdbfnum][s]
-                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
-          {
-            SequenceI asp = alignment.getSequenceAt(sp);
-            for (int r = 0; r < asp.getLength(); r++)
-            {
-              // no mapping to gaps in sequence
-              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
-              {
-                continue;
-              }
-              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-  
-              if (pos < 1 || pos == lastPos)
-                continue;
-  
-              lastPos = pos;
-  
-              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
-  
-              if (fr != null)
-                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
-              String newSelcom = (mapping[m].getChain() != " " ? ":"
-                      + mapping[m].getChain() : "")
-                      + "/"
-                      + (pdbfnum + 1)
-                      + ".1"
-                      + ";color["
-                      + col.getRed()
-                      + ","
-                      + col.getGreen()
-                      + ","
-                      + col.getBlue() + "]";
+  {
+    ArrayList<String> str = new ArrayList<String>();
+    StringBuffer command = new StringBuffer();
+
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    {
+      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
+
+      if (mapping == null || mapping.length < 1)
+        continue;
+
+      int lastPos = -1;
+      for (int s = 0; s < sequence[pdbfnum].length; s++)
+      {
+        for (int sp, m = 0; m < mapping.length; m++)
+        {
+          if (mapping[m].getSequence() == sequence[pdbfnum][s]
+                  && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+          {
+            SequenceI asp = alignment.getSequenceAt(sp);
+            for (int r = 0; r < asp.getLength(); r++)
+            {
+              // no mapping to gaps in sequence
+              if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+              {
+                continue;
+              }
+              int pos = mapping[m].getPDBResNum(asp.findPosition(r));
+
+              if (pos < 1 || pos == lastPos)
+                continue;
+
+              lastPos = pos;
+
+              Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+
+              if (fr != null)
+                col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
+              String newSelcom = (mapping[m].getChain() != " " ? ":"
+                      + mapping[m].getChain() : "")
+                      + "/"
+                      + (pdbfnum + 1)
+                      + ".1"
+                      + ";color["
+                      + col.getRed()
+                      + ","
+                      + col.getGreen()
+                      + ","
+                      + col.getBlue() + "]";
               if (command.length() > newSelcom.length()
                       && command.substring(
                               command.length() - newSelcom.length())
                               .equals(newSelcom))
-              {
-                command = VarnaCommands.condenseCommand(command, pos);
-                continue;
-              }
-              // TODO: deal with case when buffer is too large for Jmol to parse
-              // - execute command and flush
-  
-              command.append(";");
-              if (command.length()>51200)
-              {
-                // add another chunk
-                str.add(command.toString());
-                command.setLength(0);
-              }
-              command.append("select " + pos);
-              command.append(newSelcom);
-            }
-            break;
-          }
-        }
-      }
-    }
-    {
-      // add final chunk
-      str.add(command.toString());
-      command.setLength(0);
-    }
-    return str.toArray(new String[str.size()]);
-  }
-
-  public static StringBuffer condenseCommand(StringBuffer command, int pos)
-  {
-  
-    // work back to last 'select'
-    int p=command.length(),q=p;
+              {
+                command = VarnaCommands.condenseCommand(command, pos);
+                continue;
+              }
+              // TODO: deal with case when buffer is too large for Jmol to parse
+              // - execute command and flush
+
+              command.append(";");
+              if (command.length() > 51200)
+              {
+                // add another chunk
+                str.add(command.toString());
+                command.setLength(0);
+              }
+              command.append("select " + pos);
+              command.append(newSelcom);
+            }
+            break;
+          }
+        }
+      }
+    }
+    {
+      // add final chunk
+      str.add(command.toString());
+      command.setLength(0);
+    }
+    return str.toArray(new String[str.size()]);
+  }
+
+  public static StringBuffer condenseCommand(StringBuffer command, int pos)
+  {
+
+    // work back to last 'select'
+    int p = command.length(), q = p;
     do
     {
-      p-=6;
+      p -= 6;
       if (p < 1)
       {
         p = 0;
       }
       ;
-    } while ((q=command.indexOf("select",p))==-1 && p>0);
-    
-    StringBuffer sb = new StringBuffer(command.substring(0,q+7));
-  
-    command =  command.delete(0,q+7);
-  
-    String start;
-  
-    if (command.indexOf("-") > -1)
-    {
-      start = command.substring(0, command.indexOf("-"));
-    }
-    else
-    {
-      start = command.substring(0, command.indexOf(":"));
-    }
-  
-    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
-  
-    return sb;
-  }
-
-}
+    } while ((q = command.indexOf("select", p)) == -1 && p > 0);
+
+    StringBuffer sb = new StringBuffer(command.substring(0, q + 7));
+
+    command = command.delete(0, q + 7);
+
+    String start;
+
+    if (command.indexOf("-") > -1)
+    {
+      start = command.substring(0, command.indexOf("-"));
+    }
+    else
+    {
+      start = command.substring(0, command.indexOf(":"));
+    }
+
+    sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
+
+    return sb;
+  }
+
+}