JAL-2146 show Column no [Sequence no [Residue / pos]] on mouseover

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 40c311f..f20558d 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -1308,3 +1308,5 @@ status.fetching_3d_structures_for = Fetching 3D Structure for {0}
 status.obtaining_mapping_with_sifts = Obtaining mapping with SIFTS
 status.obtaining_mapping_with_nw_alignment = Obtaining mapping with NW alignment
 status.exporting_alignment_as_x_file = Exporting alignment as {0} file
+label.column = Column
+label.sequence = Sequence

diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties
index 618178d..3f04bad 100644 (file)
--- a/resources/lang/Messages_es.properties
+++ b/resources/lang/Messages_es.properties
@@ -468,8 +468,9 @@ label.create_sequence_feature = Crear funci
 label.edit_sequence = Editar secuencia
 label.edit_sequences = Editar secuencias
 label.sequence_details = Detalles de la secuencia
-label.jmol_help = Ayuda de Jmol 
-label.all = Todo
+label.jmol_help = Ayuda de Jmol
+# Todos/Todas is gender-sensitive, but currently only used for feminine (cadena / anotación)! 
+label.all = Todas
 label.sort_by = Ordenar por
 label.sort_by_score = Ordenar por puntuación
 label.sort_by_density = Ordenar por densidad
@@ -1314,3 +1315,5 @@ status.fetching_3d_structures_for_selected_entries=Buscando las estructuras 3D p
 status.fetching_dbrefs_for_sequences_without_valid_refs=Buscando referencias para {0} secuencia(s) sin referencia válida necesaria para mapeado SIFTS
 status.obtaining_mapping_with_nw_alignment=Obteniendo mapeo por alineamiento Needleman y Wunsch
 status.exporting_alignment_as_x_file = Exportando alineamiento como fichero tipo {0}
+label.column = Columna
+label.sequence = Secuencia

diff --git a/src/jalview/appletgui/AnnotationPanel.java b/src/jalview/appletgui/AnnotationPanel.java
index 77700d0..dd652b1 100755 (executable)
--- a/src/jalview/appletgui/AnnotationPanel.java
+++ b/src/jalview/appletgui/AnnotationPanel.java
@@ -22,8 +22,10 @@ package jalview.appletgui;
 
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.Color;
@@ -457,21 +459,47 @@ public class AnnotationPanel extends Panel implements AwtRenderPanelI,
       }
     }
 
-    int res = evt.getX() / av.getCharWidth() + av.getStartRes();
+    int column = evt.getX() / av.getCharWidth() + av.getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      column = av.getColumnSelection().adjustForHiddenColumns(column);
     }
 
-    if (row > -1 && res < aa[row].annotations.length
-            && aa[row].annotations[res] != null)
+    if (row > -1 && column < aa[row].annotations.length
+            && aa[row].annotations[column] != null)
     {
-      StringBuffer text = new StringBuffer("Sequence position " + (res + 1));
-      if (aa[row].annotations[res].description != null)
+      StringBuilder text = new StringBuilder();
+      text.append(MessageManager.getString("label.column")).append(" ")
+              .append(column + 1);
+      if (aa[row].annotations[column].description != null)
       {
-        text.append("  " + aa[row].annotations[res].description);
+        text.append("  ").append(aa[row].annotations[column].description);
       }
+
+      /*
+       * if the annotation is sequence-specific, show the sequence number
+       * in the alignment, and (if not a gap) the residue and position
+       */
+      SequenceI seqref = aa[row].sequenceRef;
+      if (seqref != null)
+      {
+        int seqIndex = av.getAlignment().findIndex(seqref);
+        if (seqIndex != -1)
+        {
+          text.append(", ")
+                  .append(MessageManager.getString("label.sequence"))
+                  .append(" ").append(seqIndex + 1);
+          char residue = seqref.getCharAt(column);
+          if (!Comparison.isGap(residue))
+          {
+            int residuePos = seqref.findPosition(column);
+            text.append(": ").append(residue).append(" (")
+                    .append(residuePos).append(")");
+          }
+        }
+      }
+
       ap.alignFrame.statusBar.setText(text.toString());
     }
   }

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 60c182e..398f57d 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -26,6 +26,7 @@ import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
 import java.awt.AlphaComposite;
@@ -629,10 +630,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
   }
 
   /**
-   * DOCUMENT ME!
+   * Constructs the tooltip, and constructs and displays a status message, for
+   * the current mouse position
    * 
    * @param evt
-   *          DOCUMENT ME!
    */
   @Override
   public void mouseMoved(MouseEvent evt)
@@ -658,7 +659,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       if (evt.getY() < height)
       {
         row = i;
-
         break;
       }
     }
@@ -669,64 +669,125 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       return;
     }
 
-    int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+    int column = (evt.getX() / av.getCharWidth()) + av.getStartRes();
 
     if (av.hasHiddenColumns())
     {
-      res = av.getColumnSelection().adjustForHiddenColumns(res);
+      column = av.getColumnSelection().adjustForHiddenColumns(column);
     }
 
-    if (row > -1 && aa[row].annotations != null
-            && res < aa[row].annotations.length)
+    AlignmentAnnotation ann = aa[row];
+    if (row > -1 && ann.annotations != null
+            && column < ann.annotations.length)
+    {
+      buildToolTip(ann, column, aa);
+      setStatusMessage(column, ann);
+    }
+    else
     {
-      if (aa[row].graphGroup > -1)
+      this.setToolTipText(null);
+      ap.alignFrame.statusBar.setText(" ");
+    }
+  }
+
+  /**
+   * Builds a tooltip for the annotation at the current mouse position.
+   * 
+   * @param ann
+   * @param column
+   * @param anns
+   */
+  void buildToolTip(AlignmentAnnotation ann, int column,
+          AlignmentAnnotation[] anns)
+  {
+    if (ann.graphGroup > -1)
+    {
+      StringBuilder tip = new StringBuilder(32);
+      tip.append("<html>");
+      for (int i = 0; i < anns.length; i++)
       {
-        StringBuffer tip = new StringBuffer("<html>");
-        for (int gg = 0; gg < aa.length; gg++)
+        if (anns[i].graphGroup == ann.graphGroup
+                && anns[i].annotations[column] != null)
         {
-          if (aa[gg].graphGroup == aa[row].graphGroup
-                  && aa[gg].annotations[res] != null)
+          tip.append(anns[i].label);
+          String description = anns[i].annotations[column].description;
+          if (description != null && description.length() > 0)
           {
-            tip.append(aa[gg].label + " "
-                    + aa[gg].annotations[res].description + "<br>");
+            tip.append(" ").append(description);
           }
-        }
-        if (tip.length() != 6)
-        {
-          tip.setLength(tip.length() - 4);
-          this.setToolTipText(tip.toString() + "</html>");
+          tip.append("<br>");
         }
       }
-      else if (aa[row].annotations[res] != null
-              && aa[row].annotations[res].description != null
-              && aa[row].annotations[res].description.length() > 0)
+      if (tip.length() != 6)
       {
-        this.setToolTipText(JvSwingUtils.wrapTooltip(true,
-                aa[row].annotations[res].description));
+        tip.setLength(tip.length() - 4);
+        this.setToolTipText(tip.toString() + "</html>");
       }
-      else
+    }
+    else if (ann.annotations[column] != null)
+    {
+      String description = ann.annotations[column].description;
+      if (description != null && description.length() > 0)
       {
-        // clear the tooltip.
-        this.setToolTipText(null);
+        this.setToolTipText(JvSwingUtils.wrapTooltip(true, description));
       }
+    }
+    else
+    {
+      // clear the tooltip.
+      this.setToolTipText(null);
+    }
+  }
 
-      if (aa[row].annotations[res] != null)
+  /**
+   * Constructs and displays the status bar message
+   * 
+   * @param column
+   * @param ann
+   */
+  void setStatusMessage(int column, AlignmentAnnotation ann)
+  {
+    /*
+     * show alignment column and annotation description if any
+     */
+    StringBuilder text = new StringBuilder(32);
+    text.append(MessageManager.getString("label.column")).append(" ")
+            .append(column + 1);
+
+    if (ann.annotations[column] != null)
+    {
+      String description = ann.annotations[column].description;
+      if (description != null && description.trim().length() > 0)
       {
-        StringBuffer text = new StringBuffer("Sequence position "
-                + (res + 1));
+        text.append("  ").append(description);
+      }
+    }
 
-        if (aa[row].annotations[res].description != null)
+    /*
+     * if the annotation is sequence-specific, show the sequence number
+     * in the alignment, and (if not a gap) the residue and position
+     */
+    SequenceI seqref = ann.sequenceRef;
+    if (seqref != null)
+    {
+      int seqIndex = av.getAlignment().findIndex(seqref);
+      if (seqIndex != -1)
+      {
+        text.append(", ")
+                .append(MessageManager.getString("label.sequence"))
+                .append(" ")
+                .append(seqIndex + 1);
+        char residue = seqref.getCharAt(column);
+        if (!Comparison.isGap(residue))
         {
-          text.append("  " + aa[row].annotations[res].description);
+          int residuePos = seqref.findPosition(column);
+          text.append(": ").append(residue).append(" (")
+                  .append(residuePos).append(")");
         }
-
-        ap.alignFrame.statusBar.setText(text.toString());
       }
     }
-    else
-    {
-      this.setToolTipText(null);
-    }
+
+    ap.alignFrame.statusBar.setText(text.toString());
   }
 
   /**