From 969d3ba3a4224ab48fe87dc85248ae8a119b2e2c Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 23 Mar 2007 17:26:20 +0000
Subject: [PATCH] updates to console

---
 src/jalview/appletgui/AppletJmol.java |   82 ++++++++++++++++++++++++---------
 1 file changed, 61 insertions(+), 21 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index b03775b..9ff3078 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -55,6 +55,7 @@ public class AppletJmol extends Frame
   String fileLoadingError;
   boolean loadedInline;
   PDBEntry pdbentry;
+  boolean colourBySequence = true;
 
   public AppletJmol(PDBEntry pdbentry,
                     SequenceI[] seq,
@@ -224,9 +225,7 @@ public class AppletJmol extends Frame
         && scriptWindow.isVisible())
     {
       viewer.evalString(inputLine.getText());
-
-      history.append("\n"+inputLine.getText());
-
+      history.append("\n$ "+inputLine.getText());
       inputLine.setText("");
     }
 
@@ -317,6 +316,10 @@ public class AppletJmol extends Frame
   FeatureRenderer fr;
   public void colourBySequence(AlignmentPanel ap)
   {
+    if(!colourBySequence)
+      return;
+
+
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     if (mapping.length < 1)
@@ -338,6 +341,7 @@ public class AppletJmol extends Frame
 
     StringBuffer command = new StringBuffer();
 
+    int lastPos = -1;
     for (int s = 0; s < sequence.length; s++)
     {
       for (int m = 0; m < mapping.length; m++)
@@ -349,8 +353,25 @@ public class AppletJmol extends Frame
             int pos = mapping[m].getPDBResNum(
                 sequence[s].findPosition(r));
 
-            if (pos < 1)
+            if (pos < 1 || pos==lastPos)
+              continue;
+
+            lastPos = pos;
+
+            Color col = sr.getResidueBoxColour(sequence[s], r);
+
+            if (showFeatures)
+              col = fr.findFeatureColour(col, sequence[s], r);
+
+            if (command.toString().endsWith(":" + mapping[m].getChain()+
+                                            ";color["
+                                            + col.getRed() + ","
+                                            + col.getGreen() + ","
+                                            + col.getBlue() + "]"))
+            {
+              command = condenseCommand(command.toString(), pos);
               continue;
+            }
 
             command.append(";select " + pos);
 
@@ -359,17 +380,13 @@ public class AppletJmol extends Frame
               command.append(":" + mapping[m].getChain());
             }
 
-            Color col = sr.getResidueBoxColour(sequence[s], r);
-
-            if (showFeatures)
-              col = fr.findFeatureColour(col, sequence[s], r);
-
-            command.append("; color ["
-                           + col.getRed() + ","
-                           + col.getGreen() + ","
-                           + col.getBlue() + "]");
+            command.append(";color["
+                             + col.getRed() + ","
+                             + col.getGreen() + ","
+                             + col.getBlue() + "]");
 
           }
+          break;
         }
       }
     }
@@ -377,6 +394,29 @@ public class AppletJmol extends Frame
     viewer.evalStringQuiet(command.toString());
   }
 
+  StringBuffer condenseCommand(String command, int pos)
+  {
+
+    StringBuffer sb = new StringBuffer(command.substring(0, command.lastIndexOf("select")+7));
+
+    command = command.substring(sb.length());
+
+    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;
+  }
+
   /////////////////////////////////
   //JmolStatusListener
 
@@ -388,9 +428,7 @@ public class AppletJmol extends Frame
   }
 
   public void createImage(String file, String type, int quality)
-  {
-    System.out.println("JMOL CREATE IMAGE");
-  }
+  {}
 
   public void setCallbackFunction(String callbackType,
                                   String callbackFunction)
@@ -425,7 +463,6 @@ public class AppletJmol extends Frame
                                 pdbentry.getFile(),
                                 AppletFormatAdapter.PASTE);
         pdbentry.setFile("INLINE"+pdb.id);
-
       }
       else
       {
@@ -487,14 +524,17 @@ public class AppletJmol extends Frame
 
   public void sendConsoleMessage(String strStatus)
   {
-   // if (scriptWindow != null)
-   //   scriptWindow.sendConsoleMessage(strStatus);
+    if(history!=null && strStatus!=null
+       && !strStatus.equals("Script completed"))
+    {
+      history.append("\n"+strStatus);
+    }
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
-  //  if (scriptWindow != null)
-  //    scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+   // if (scriptWindow != null)
+   //   scriptWindow.notifyScriptTermination(strStatus, msWalltime);
   }
 
   public void handlePopupMenu(int x, int y)
-- 
1.7.10.2