import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.AlphaComposite;
}
}
else
- // HELIX OR SHEET
+ // HELIX, SHEET or STEM
{
char type = 0;
String symbol = "\u03B1";
}
}
+
av.getAlignment().validateAnnotation(aa[activeRow]);
ap.alignmentChanged();
-
+ ap.alignFrame.setMenusForViewport();
adjustPanelHeight();
repaint();
}
/**
- * 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)
if (evt.getY() < height)
{
row = i;
-
break;
}
}
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);
+ }
+
+ AlignmentAnnotation ann = aa[row];
+ if (row > -1 && ann.annotations != null
+ && column < ann.annotations.length)
+ {
+ buildToolTip(ann, column, aa);
+ setStatusMessage(column, ann);
+ }
+ else
+ {
+ this.setToolTipText(null);
+ ap.alignFrame.statusBar.setText(" ");
}
+ }
- if (row > -1 && aa[row].annotations != null
- && res < aa[row].annotations.length)
+ /**
+ * 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)
{
- if (aa[row].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());
}
/**
git://source.jalview.org / jalview.git / blobdiff