JAL-2009 added programmatic custom feature setting to show insertion position for...

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 5df38d6..45e77ba 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -375,4 +375,6 @@ public interface AlignViewportI extends ViewStyleI
    * Set whether view should scroll to show the highlighted region of a sequence
    */
   void setFollowHighlight(boolean b);
+
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
 }

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 7ef2d59..09e6562 100644 (file)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -22,6 +22,7 @@ package jalview.appletgui;
 
 import jalview.analysis.NJTree;
 import jalview.api.AlignViewportI;
+import jalview.api.FeatureSettingsModelI;
 import jalview.bin.JalviewLite;
 import jalview.commands.CommandI;
 import jalview.datamodel.AlignmentI;
@@ -57,6 +58,7 @@ public class AlignViewport extends AlignmentViewport implements
 
   private AnnotationColumnChooser annotationColumnSelectionState;
 
+  @Override
   public void finalize()
   {
     applet = null;
@@ -325,6 +327,7 @@ public class AlignViewport extends AlignmentViewport implements
     return followSelection;
   }
 
+  @Override
   public void sendSelection()
   {
     getStructureSelectionManager().sendSelection(
@@ -378,6 +381,7 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -392,6 +396,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;
@@ -470,4 +475,18 @@ public class AlignViewport extends AlignmentViewport implements
     }
   }
 
+  /**
+   * Applies the supplied feature settings descriptor to currently known
+   * features. This supports an 'initial configuration' of feature colouring
+   * based on a preset or user favourite. This may then be modified in the usual
+   * way using the Feature Settings dialogue.
+   * 
+   * @param featureSettings
+   */
+  @Override
+  public void applyFeaturesStyle(FeatureSettingsModelI featureSettings)
+  {
+    // TODO implement for applet
+  }
+
 }

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index ebc2c21..cd875c9 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -228,7 +228,7 @@ public class Cache
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
 
-  private final static String DEFAULT_STRUCTURE_FOMART = DBRefSource.MMCIF;
+  private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.MMCIF;
 
   /**
    * Initialises the Jalview Application Log
@@ -427,7 +427,7 @@ public class Cache
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
     Pdb.setCurrentDefaultFomart(jalview.bin.Cache.getDefault(
-            "DEFAULT_STRUCTURE_FOMART", DEFAULT_STRUCTURE_FOMART));
+            "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index c0e59a4..76f1041 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
@@ -253,12 +254,19 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
     {
       String title = MessageManager.formatMessage(
               "label.input_cut_paste_params", new String[] { format });
+      FeatureSettingsModelI proxyColourScheme = source
+              .getFeatureColourScheme();
+
       /*
        * if the view panel was closed its alignment is nulled
        * and this is an orphaned cut and paste window
        */
       if (viewport != null && viewport.getAlignment() != null)
       {
+        if (proxyColourScheme != null)
+        {
+          viewport.applyFeaturesStyle(proxyColourScheme);
+        }
         ((AlignViewport) viewport).addAlignment(al, title);
       }
       else
@@ -297,7 +305,10 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
             af.getViewport().setShowSequenceFeatures(true);
           }
         }
-
+        if (proxyColourScheme != null)
+        {
+          af.getViewport().applyFeaturesStyle(proxyColourScheme);
+        }
         af.currentFileFormat = format;
         Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
                 AlignFrame.DEFAULT_HEIGHT);

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 8f0d210..27f60ea 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1065,13 +1065,6 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       {
         new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE,
                 format);
-        // viewport.setShowSequenceFeatures(JSONFile.isSeqFeaturesEnabled());
-        // AlignFrame af = viewport.getAlignPanel().alignFrame;
-        // if (af != null)
-        // {
-        // af.changeColour(JSONFile.getColourScheme());
-        // af.setMenusForViewport();
-        // }
       }
       else
       {

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b1944b4..b449d19 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -21,6 +21,7 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.api.FeaturesSourceI;
 import jalview.bin.Jalview;
@@ -362,8 +363,14 @@ public class FileLoader implements Runnable
             }
           }
 
+          FeatureSettingsModelI proxyColourScheme = source
+                  .getFeatureColourScheme();
           if (viewport != null)
           {
+            if (proxyColourScheme != null)
+            {
+              viewport.applyFeaturesStyle(proxyColourScheme);
+            }
             // append to existing alignment
             viewport.addAlignment(al, title);
           }
@@ -407,7 +414,11 @@ public class FileLoader implements Runnable
             {
               alignFrame.setFileName(file, format);
             }
-
+            if (proxyColourScheme != null)
+            {
+              alignFrame.getViewport()
+                      .applyFeaturesStyle(proxyColourScheme);
+            }
             alignFrame.statusBar.setText(MessageManager.formatMessage(
                     "label.successfully_loaded_file",
                     new String[] { title }));

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index 61f5127..fddb565 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -23,6 +23,7 @@ package jalview.io;
 import jalview.api.AlignExportSettingI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
+import jalview.api.FeatureSettingsModelI;
 import jalview.util.MessageManager;
 
 import java.io.BufferedReader;
@@ -613,4 +614,15 @@ public class FileParse
     }
     // could also set export/import settings
   }
+
+  /**
+   * Returns the preferred feature colour configuration if there is one, else
+   * null
+   * 
+   * @return
+   */
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return null;
+  }
 }

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 954d12e..e31e78d 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -22,6 +22,7 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -124,6 +125,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
             "Print method of HtmlFile is not supported!");
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -134,6 +136,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
+  @Override
   public String getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -144,6 +147,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.globalColourScheme = globalColourScheme;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -154,6 +158,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     return hiddenSequences;
@@ -170,4 +175,19 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     return displayedFeatures;
   }
 
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
+
 }

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 1038925..36980f8 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -26,6 +26,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.bin.BuildDetails;
 import jalview.datamodel.AlignmentAnnotation;
@@ -709,6 +710,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
+  @Override
   public String getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -730,6 +732,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.displayedFeatures = displayedFeatures;
   }
 
+  @Override
   public void configureForView(AlignmentViewPanel avpanel)
   {
     super.configureForView(avpanel);
@@ -755,6 +758,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -775,6 +779,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     return hiddenColumns;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -785,6 +790,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     if (hiddenSequences == null || hiddenSequences.isEmpty())
@@ -864,4 +870,19 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
       this.exportJalviewSettings = exportJalviewSettings;
     }
   }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }

diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
new file mode 100644 (file)
index 0000000..a422a00
--- /dev/null
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -0,0 +1,63 @@
+package jalview.io;
+
+import jalview.api.FeatureColourI;
+import jalview.schemes.FeatureColourAdapter;
+import jalview.schemes.FeatureSettingsAdapter;
+import jalview.ws.dbsources.Pdb;
+
+import java.awt.Color;
+
+public class PDBFeatureSettings extends FeatureSettingsAdapter
+{
+
+  @Override
+  public boolean isFeatureDisplayed(String type)
+  {
+    return type.equalsIgnoreCase(Pdb.FEATURE_INSERTION)
+            || type.equalsIgnoreCase(Pdb.FEATURE_RES_NUM);
+  }
+
+  @Override
+  public FeatureColourI getFeatureColour(String type)
+  {
+    if (type.equalsIgnoreCase(Pdb.FEATURE_INSERTION))
+    {
+      return new FeatureColourAdapter()
+      {
+
+        @Override
+        public Color getColour()
+        {
+          return Color.RED;
+        }
+      };
+    }
+    return null;
+  }
+
+  /**
+   * Order to render insertion after ResNum
+   */
+  @Override
+  public int compare(String feature1, String feature2)
+  {
+    if (feature1.equalsIgnoreCase(Pdb.FEATURE_INSERTION))
+    {
+      return +1;
+    }
+    if (feature2.equalsIgnoreCase(Pdb.FEATURE_INSERTION))
+    {
+      return -1;
+    }
+    if (feature1.equalsIgnoreCase(Pdb.FEATURE_RES_NUM))
+    {
+      return +1;
+    }
+    if (feature2.equalsIgnoreCase(Pdb.FEATURE_RES_NUM))
+    {
+      return -1;
+    }
+    return 0;
+  }
+}
+

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 7262443..fd488f0 100644 (file)
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -1,6 +1,7 @@
 package jalview.io;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -397,4 +398,19 @@ public abstract class StructureFile extends AlignFile
   {
     this.dbRefType = dbRefType;
   }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 358c838..2421b82 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -20,6 +20,7 @@
  */
 package jalview.ws.dbsources;
 
+import jalview.api.FeatureSettingsModelI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -27,6 +28,7 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.FormatAdapter;
+import jalview.io.PDBFeatureSettings;
 import jalview.util.MessageManager;
 import jalview.ws.ebi.EBIFetchClient;
 
@@ -47,6 +49,10 @@ public class Pdb extends EbiFileRetrievedProxy
     super();
   }
 
+  public static final String FEATURE_INSERTION = "INSERTION";
+
+  public static final String FEATURE_RES_NUM = "RESNUM";
+
   private static String currentDefaultFomart = DBRefSource.MMCIF;
 
   /*
@@ -266,4 +272,19 @@ public class Pdb extends EbiFileRetrievedProxy
   {
     Pdb.currentDefaultFomart = currentDefaultFomart;
   }
+
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
 }