1.1 compatible, formatting changes

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 06b62c6..1bf8567 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -60,7 +60,7 @@ public class ClustalxColourScheme implements ColourSchemeI
       String seq;\r
       while(j < seqs.size())\r
       {\r
-        seq = ( (SequenceI) seqs.get(j)).getSequence();\r
+        seq = ( (SequenceI) seqs.elementAt(j)).getSequence();\r
         int end_j = seq.length()-1;\r
         for (i = start; i <= end_j; i++)\r
         {\r

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 6831ec2..6488b8d 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,100 +1,100 @@
-package jalview.schemes;
-
-public class ColourSchemeProperty
-{
-  public static final int CLUSTAL = 0;
-  public static final int BLOSUM = 1;
-  public static final int PID = 2;
-  public static final int ZAPPO = 3;
-  public static final int HYDROPHOBIC=4;
-  public static final int HELIX=5;
-  public static final int STRAND=6;
-  public static final int TURN = 7;
-  public static final int BURIED = 8;
-  public static final int NUCLEOTIDE = 9;
-  public static final int USER_DEFINED = 10;
-  public static final int NONE = 11;
-
-  public static int getColourIndexFromName(String name)
-  {
-    int ret=11;
-    if(name.equals("Clustal"))
-      ret = CLUSTAL;
-    else if(name.equals("Blosum62"))
-      ret = BLOSUM;
-    else if(name.equals("% Identity"))
-      ret = PID;
-    else if(name.equals("Zappo"))
-      ret = ZAPPO;
-    else if(name.equals("Hydrophobic"))
-      ret = HYDROPHOBIC;
-    else if(name.equals("Helix Propensity"))
-      ret = HELIX;
-    else if(name.equals("Strand Propensity"))
-      ret = STRAND;
-    else if(name.equals("Turn Propensity"))
-      ret = TURN;
-    else if(name.equals("Buried Index"))
-      ret = BURIED;
-    else if(name.equals("Nucleotide"))
-      ret = NUCLEOTIDE;
-    else if(name.equals("User Defined"))
-      ret =  USER_DEFINED;
-
-    return ret;
-  }
-
-  public static String getColourName(int index)
-  {
-    String ret=null;
-    switch(index)
-    {
-      case CLUSTAL: ret = "Clustal";    break;
-      case BLOSUM:  ret = "Blosum62";   break;
-      case PID:     ret = "% Identity"; break;
-      case ZAPPO:   ret = "Zappo";      break;
-      case HYDROPHOBIC: ret="Hydrophobic";break;
-      case HELIX:   ret="Helix Propensity";break;
-      case STRAND:  ret="Strand Propensity";break;
-      case TURN:    ret="Turn Propensity";break;
-      case BURIED:  ret="Buried Index";break;
-      case NUCLEOTIDE:ret="Nucleotide"; break;
-      case USER_DEFINED:ret="User Defined";break;
-      default: ret = "None"; break;
-    }
-    return ret;
-  }
-
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)
-  {
-    return getColour(al, getColourIndexFromName(name));
-  }
-
-  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)
-  {
-    ColourSchemeI cs = null;
-    switch(index)
-    {
-      case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;
-      case BLOSUM: cs = new Blosum62ColourScheme(); break;
-      case PID: cs = new PIDColourScheme();  break;
-      case ZAPPO: cs = new ZappoColourScheme(); break;
-      case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;
-      case HELIX: cs = new HelixColourScheme(); break;
-      case STRAND: cs = new StrandColourScheme(); break;
-      case TURN: cs = new TurnColourScheme(); break;
-      case BURIED: cs = new BuriedColourScheme(); break;
-      case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;
-      case USER_DEFINED:
-        if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)
-        {
-          cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));
-        }
-        break;
-
-      default: break;
-    }
-
-    return cs;
-  }
-}
+package jalview.schemes;\r
+\r
+public class ColourSchemeProperty\r
+{\r
+  public static final int CLUSTAL = 0;\r
+  public static final int BLOSUM = 1;\r
+  public static final int PID = 2;\r
+  public static final int ZAPPO = 3;\r
+  public static final int HYDROPHOBIC=4;\r
+  public static final int HELIX=5;\r
+  public static final int STRAND=6;\r
+  public static final int TURN = 7;\r
+  public static final int BURIED = 8;\r
+  public static final int NUCLEOTIDE = 9;\r
+  public static final int USER_DEFINED = 10;\r
+  public static final int NONE = 11;\r
+\r
+  public static int getColourIndexFromName(String name)\r
+  {\r
+    int ret=11;\r
+    if(name.equalsIgnoreCase("Clustal"))\r
+      ret = CLUSTAL;\r
+    else if(name.equalsIgnoreCase("Blosum62"))\r
+      ret = BLOSUM;\r
+    else if(name.equalsIgnoreCase("% Identity"))\r
+      ret = PID;\r
+    else if(name.equalsIgnoreCase("Zappo"))\r
+      ret = ZAPPO;\r
+    else if(name.equalsIgnoreCase("Hydrophobic"))\r
+      ret = HYDROPHOBIC;\r
+    else if(name.equalsIgnoreCase("Helix Propensity"))\r
+      ret = HELIX;\r
+    else if(name.equalsIgnoreCase("Strand Propensity"))\r
+      ret = STRAND;\r
+    else if(name.equalsIgnoreCase("Turn Propensity"))\r
+      ret = TURN;\r
+    else if(name.equalsIgnoreCase("Buried Index"))\r
+      ret = BURIED;\r
+    else if(name.equalsIgnoreCase("Nucleotide"))\r
+      ret = NUCLEOTIDE;\r
+    else if(name.equalsIgnoreCase("User Defined"))\r
+      ret =  USER_DEFINED;\r
+\r
+    return ret;\r
+  }\r
+\r
+  public static String getColourName(int index)\r
+  {\r
+    String ret=null;\r
+    switch(index)\r
+    {\r
+      case CLUSTAL: ret = "Clustal";    break;\r
+      case BLOSUM:  ret = "Blosum62";   break;\r
+      case PID:     ret = "% Identity"; break;\r
+      case ZAPPO:   ret = "Zappo";      break;\r
+      case HYDROPHOBIC: ret="Hydrophobic";break;\r
+      case HELIX:   ret="Helix Propensity";break;\r
+      case STRAND:  ret="Strand Propensity";break;\r
+      case TURN:    ret="Turn Propensity";break;\r
+      case BURIED:  ret="Buried Index";break;\r
+      case NUCLEOTIDE:ret="Nucleotide"; break;\r
+      case USER_DEFINED:ret="User Defined";break;\r
+      default: ret = "None"; break;\r
+    }\r
+    return ret;\r
+  }\r
+\r
+  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, String name)\r
+  {\r
+    return getColour(al, getColourIndexFromName(name));\r
+  }\r
+\r
+  public static ColourSchemeI getColour(jalview.datamodel.AlignmentI al, int index)\r
+  {\r
+    ColourSchemeI cs = null;\r
+    switch(index)\r
+    {\r
+      case CLUSTAL: cs = new ClustalxColourScheme(al.getSequences(), al.getWidth()); break;\r
+      case BLOSUM: cs = new Blosum62ColourScheme(); break;\r
+      case PID: cs = new PIDColourScheme();  break;\r
+      case ZAPPO: cs = new ZappoColourScheme(); break;\r
+      case HYDROPHOBIC: cs = new HydrophobicColourScheme(); break;\r
+      case HELIX: cs = new HelixColourScheme(); break;\r
+      case STRAND: cs = new StrandColourScheme(); break;\r
+      case TURN: cs = new TurnColourScheme(); break;\r
+      case BURIED: cs = new BuriedColourScheme(); break;\r
+      case NUCLEOTIDE: cs = new NucleotideColourScheme(); break;\r
+      case USER_DEFINED:\r
+       // if(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR")!=null)\r
+        {\r
+       //   cs = jalview.gui.UserDefinedColours.loadDefaultColours(jalview.bin.Cache.getProperty("USER_DEFINED_COLOUR"));\r
+        }\r
+        break;\r
+\r
+      default: break;\r
+    }\r
+\r
+    return cs;\r
+  }\r
+}\r

diff --git a/src/jalview/schemes/ConservationColourScheme.java b/src/jalview/schemes/ConservationColourScheme.java
index 88a6686..6394124 100755 (executable)
--- a/src/jalview/schemes/ConservationColourScheme.java
+++ b/src/jalview/schemes/ConservationColourScheme.java
@@ -1,86 +1,87 @@
-/* Jalview - a java multiple alignment editor
- * Copyright (C) 1998  Michele Clamp
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
- */
-
-package jalview.schemes;
-import java.awt.*;
-import jalview.analysis.*;
-import java.util.Vector;
-
-public class ConservationColourScheme extends ResidueColourScheme {
-  public Conservation conserve;
-  public ColourSchemeI cs;
-  public int inc = 30;
-
-  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)
-  {
-    super();
-    conserve = cons;
-    cs = oldcs;
-  }
-
-  public void setConsensus(Vector consensus)
-  {
-    this.consensus = consensus;
-    cs.setConsensus(consensus);
-  }
-
-   public Color findColour(String s, int i)
-   {
-     Color c = Color.white;
-     if (cs == null)
-       return c;
-
-     char ch = conserve.getConsSequence().getSequence().charAt(i);
-     if (ch == '*' || ch == '+')
-     {
-       c = cs.findColour(s, i);
-     }
-     else
-     {
-       int tmp = 10;
-       int t = 0;
-       if (!jalview.util.Comparison.isGap(ch))
-         t = Integer.parseInt(ch + "");
-
-       c = cs.findColour(s, i);
-
-       while (tmp >= t)
-       {
-         c = lighter(c, inc);
-         tmp--;
-       }
-
-     }
-
-   return c;
-   }
-
-
-  public Color lighter(Color c, int inc) {
-    int red = c.getRed();
-    int blue = c.getBlue();
-    int green = c.getGreen();
-
-    if (red < 255-inc) { red = red +inc;} else {red = 255;}
-    if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}
-    if (green < 255-inc) { green = green +inc;} else {green = 255;}
-
-    return new Color(red,green,blue);
-  }
-
-}
+/* Jalview - a java multiple alignment editor\r
+ * Copyright (C) 1998  Michele Clamp\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.\r
+ */\r
+\r
+package jalview.schemes;\r
+import java.awt.*;\r
+import jalview.analysis.*;\r
+import java.util.Vector;\r
+\r
+public class ConservationColourScheme extends ResidueColourScheme {\r
+  public Conservation conserve;\r
+  public ColourSchemeI cs;\r
+  public int inc = 30;\r
+\r
+  public ConservationColourScheme(Conservation cons, ColourSchemeI oldcs)\r
+  {\r
+    super();\r
+    conserve = cons;\r
+    cs = oldcs;\r
+  }\r
+\r
+  public void setConsensus(Vector consensus)\r
+  {\r
+    this.consensus = consensus;\r
+    if(cs!=null)\r
+      cs.setConsensus(consensus);\r
+  }\r
+\r
+   public Color findColour(String s, int i)\r
+   {\r
+     Color c = Color.white;\r
+     if (cs == null)\r
+       return c;\r
+\r
+     char ch = conserve.getConsSequence().getSequence().charAt(i);\r
+     if (ch == '*' || ch == '+')\r
+     {\r
+       c = cs.findColour(s, i);\r
+     }\r
+     else\r
+     {\r
+       int tmp = 10;\r
+       int t = 0;\r
+       if (!jalview.util.Comparison.isGap(ch))\r
+         t = Integer.parseInt(ch + "");\r
+\r
+       c = cs.findColour(s, i);\r
+\r
+       while (tmp >= t)\r
+       {\r
+         c = lighter(c, inc);\r
+         tmp--;\r
+       }\r
+\r
+     }\r
+\r
+   return c;\r
+   }\r
+\r
+\r
+  public Color lighter(Color c, int inc) {\r
+    int red = c.getRed();\r
+    int blue = c.getBlue();\r
+    int green = c.getGreen();\r
+\r
+    if (red < 255-inc) { red = red +inc;} else {red = 255;}\r
+    if (blue < 255-inc) { blue = blue +inc;} else {blue = 255;}\r
+    if (green < 255-inc) { green = green +inc;} else {green = 255;}\r
+\r
+    return new Color(red,green,blue);\r
+  }\r
+\r
+}\r