From 58f946af1280918a6f2893534e66104bc20a52c7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 5 Dec 2005 13:39:56 +0000
Subject: [PATCH] Save Feature Rendering

---
 src/jalview/gui/AlignFrame.java      |   10 --------
 src/jalview/gui/FeatureSettings.java |   22 ++++++++++++------
 src/jalview/gui/Jalview2XML.java     |   42 ++++++++++++++++++++++++++++++++++
 src/jalview/gui/SequenceFetcher.java |   16 +++++++++----
 4 files changed, 68 insertions(+), 22 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index adc2195..86d7cb6 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1204,16 +1204,6 @@ public class AlignFrame
    if(alignPanel.overviewPanel!=null)
      alignPanel.overviewPanel.updateOverviewImage();
 
-  Provenance prov = viewport.alignment.getProvenance();
-  if(prov == null)
-   {
-     prov = new Provenance();
-     viewport.alignment.setProvenance(prov);
-   }
-
-   prov.addEntry("Me",
-       "Edited in Jalview", new java.util.Date(), "myID");
-
    alignPanel.repaint();
  }
 
diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index b8b623d..5325180 100755
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -145,8 +145,13 @@ public class FeatureSettings extends JPanel
     int fSize = allFeatures.size();
 
     String type;
+    boolean originalExists = false;
+    if(originalData!=null)
+      originalExists = true;
+    else
+      originalData = new Object[fSize][3];
+
     Object [][] data = new Object[fSize][3];
-    originalData = new Object[fSize][3];
     for(int i=0; i<fSize; i++)
     {
       type = allFeatures.elementAt(i).toString();
@@ -158,12 +163,15 @@ public class FeatureSettings extends JPanel
       else
         data[i][2] = new Boolean(true);
 
-      originalData[i][0]=type;
-      originalData[i][1]=col;
-      if(fr.featuresDisplayed!=null)
-         originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
-      else
-        originalData[i][2] = new Boolean(true);
+      if(!originalExists)
+      {
+        originalData[i][0] = type;
+        originalData[i][1] = col;
+        if (fr.featuresDisplayed != null)
+          originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));
+        else
+          originalData[i][2] = new Boolean(true);
+      }
     }
     ////////////////////////////////////
         //Now build the table
diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index bbe3389..08b3903 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -452,8 +452,33 @@ public class Jalview2XML
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
 
+        if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
+        {
+          jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+
+          Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+          while (e.hasMoreElements())
+          {
+            String type = e.nextElement().toString();
+            Setting setting = new Setting();
+            setting.setType(type);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
+                );
+            setting.setDisplay(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)
+                );
+
+            fs.addSetting(setting);
+
+          }
+          jms.setFeatureSettings(fs);
+
+        }
+
         jms.addViewport(view);
 
+
         object.setJalviewModelSequence(jms);
         object.getVamsasModel().addSequenceSet(vamsasSet);
 
@@ -711,6 +736,7 @@ public class Jalview2XML
 
         AlignFrame af = new AlignFrame(al);
 
+
         //  af.changeColour() );
         /////////////////////////
         //LOAD GROUPS
@@ -850,6 +876,22 @@ public class Jalview2XML
            af.sequenceFeatures.setSelected(true);
         }
 
+        if(jms.getFeatureSettings()!=null)
+        {
+          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();
+         // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
+         // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+         for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
+         {
+           Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
+               new java.awt.Color(setting.getColour()));
+           if(setting.getDisplay())
+             af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());
+         }
+        }
+
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());
 
diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 75ff09c..28d7002 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -48,7 +48,13 @@ public class SequenceFetcher
       throws Exception
   {
     this.setLayout(gridBagLayout1);
+    DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+    dlcr.setHorizontalAlignment(DefaultListCellRenderer.CENTER);
+    database.setRenderer(dlcr);
+
     database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    database.setMinimumSize(new Dimension(160, 21));
+    database.setPreferredSize(new Dimension(160, 21));
     jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
     jLabel1.setText(
         "Separate multiple accession ids with semi colon \";\"");
@@ -82,16 +88,16 @@ public class SequenceFetcher
                                              , GridBagConstraints.WEST,
                                              GridBagConstraints.NONE,
                                              new Insets(7, 4, 0, 6), 77, 6));
-    this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
-                                               , GridBagConstraints.WEST,
-                                               GridBagConstraints.HORIZONTAL,
-                                               new Insets(0, 0, 0, 6), 221, 1));
     this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
                                              , GridBagConstraints.WEST,
                                              GridBagConstraints.BOTH,
                                              new Insets(7, -2, 7, 12), 241, -2));
+    this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
+                                               , GridBagConstraints.WEST,
+                                               GridBagConstraints.HORIZONTAL,
+                                               new Insets(0, 0, 0, 6), 200, 1));
     this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
-                                              , GridBagConstraints.CENTER,
+                                              , GridBagConstraints.WEST,
                                               GridBagConstraints.NONE,
                                               new Insets(0, 4, 0, 0), 1, 0));
   }
-- 
1.7.10.2