From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 28 Apr 2005 15:33:12 +0000 (+0000)
Subject: Viewport now looks at preferences when loading up
X-Git-Tag: Release_2_0~359
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ebb52a433edbbdbd31ab82cbb1c59fc116a72b1d;p=jalview.git

Viewport now looks at preferences when loading up
---

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7fd7461..a135620 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -6,6 +6,7 @@ import jalview.analysis.NJTree;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import java.util.*;
+import jalview.bin.Cache;
 
 public class AlignViewport
 {
@@ -23,6 +24,9 @@ public class AlignViewport
   boolean renderGaps = true;
   boolean showSequenceFeatures = false;
   boolean showAnnotation = true;
+  boolean showConservation = true;
+  boolean showQuality = true;
+  boolean showIdentity = true;
 
   boolean colourAppliesToAllGroups = true;
   ColourSchemeI globalColourScheme = null;
@@ -53,21 +57,67 @@ public class AlignViewport
   boolean scaleRightWrapped = true;
 
 
-  public AlignViewport(AlignmentI al,
-                       boolean showText,
-                       boolean showBoxes,
-                       boolean wrapAlignment) {
-
+  public AlignViewport(AlignmentI al)
+  {
+    setAlignment(al);
     this.startRes = 0;
     this.endRes = al.getWidth()-1;
     this.startSeq = 0;
     this.endSeq = al.getHeight()-1;
-    this.showText = showText;
-    this.showBoxes = showBoxes;
-    this.wrapAlignment = wrapAlignment;
 
-    setAlignment(al);
-    setFont( font );
+    updateFromPreferences();
+
+  }
+
+  public void updateFromPreferences()
+  {
+    String string = Cache.getProperty("SHOW_FULL_ID");
+    if(string!=null)
+      showFullId = Boolean.valueOf(string).booleanValue();
+
+    string = Cache.getProperty("SHOW_ANNOTATIONS");
+        if(string!=null)
+      showAnnotation = Boolean.valueOf(string).booleanValue();
+
+    string = Cache.getProperty("SHOW_CONSERVATION");
+        if(string!=null)
+      showConservation = Boolean.valueOf(string).booleanValue();
+    string = Cache.getProperty("SHOW_QUALITY");
+        if(string!=null)
+      showQuality = Boolean.valueOf(string).booleanValue();
+    string = Cache.getProperty("SHOW_IDENTITY");
+        if(string!=null)
+      showIdentity = Boolean.valueOf(string).booleanValue();
+
+    string = Cache.getProperty("SHOW_FULL_ID");
+      if(string!=null)
+        showFullId = Boolean.valueOf(string).booleanValue();
+
+  String fontName = Cache.getProperty("FONT_NAME");
+  String fontStyle= Cache.getProperty("FONT_STYLE");
+  String fontSize = Cache.getProperty("FONT_SIZE");
+  if(fontName!=null && fontStyle!=null && fontSize!=null)
+      setFont( new Font(fontName,Integer.parseInt(fontStyle),Integer.parseInt(fontSize)) );
+  else
+      setFont( font );
+
+    string = Cache.getProperty("GAP_SYMBOL");
+    if(string!=null)
+      alignment.setGapCharacter( string.charAt(0) );
+
+
+    // We must set conservation and consensus before setting colour,
+    // as Blosum and Clustal require this to be done
+    updateConservation();
+    updateConsensus();
+    string = Cache.getProperty("DEFAULT_COLOUR");
+    if(string!=null)
+    {
+      globalColourScheme = ColourSchemeProperty.getColour(alignment, string);
+      if(globalColourScheme!=null)
+        globalColourScheme.setConsensus( vconsensus );
+   }
+
  }
 
  public void showSequenceFeatures(boolean b)
@@ -137,6 +187,7 @@ public class AlignViewport
                                              0f, // cons.qualityRange[0].floatValue(),
                                              11f, // cons.qualityRange[1].floatValue()
                                              1);
+      if(showConservation)
       alignment.addAnnotation(conservation);
       quality = new AlignmentAnnotation("Quality",
                                         "Alignment Quality based on Blosum62 scores",
@@ -144,11 +195,13 @@ public class AlignViewport
                                         cons.qualityRange[0].floatValue(),
                                         cons.qualityRange[1].floatValue(),
                                         1);
-      alignment.addAnnotation(quality);
+      if(showQuality)
+        alignment.addAnnotation(quality);
     }
     else {
       conservation.annotations = annotations;
       quality.annotations = qannotations;
+      quality.graphMax = cons.qualityRange[1].floatValue();
     }
 
 
@@ -198,7 +251,8 @@ public class AlignViewport
      {
        consensus = new AlignmentAnnotation("% Identity",
                                            "PID", annotations, 0f, 100f, 1);
-       alignment.addAnnotation(consensus);
+       if(showIdentity)
+         alignment.addAnnotation(consensus);
      }
      else
        consensus.annotations = annotations;