import jalview.datamodel.SequenceI;
import jalview.renderer.AnnotationRenderer;
import jalview.renderer.AwtRenderPanelI;
+import jalview.schemes.ResidueProperties;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import java.awt.event.MouseWheelEvent;
import java.awt.event.MouseWheelListener;
import java.awt.image.BufferedImage;
+import java.util.Collections;
+import java.util.List;
import javax.swing.JColorChooser;
import javax.swing.JMenuItem;
aa[activeRow].annotations = anot;
}
- if (evt.getActionCommand().equals(REMOVE))
+ String action = evt.getActionCommand();
+ if (action.equals(REMOVE))
{
- for (int sel : av.getColumnSelection().getSelected())
+ for (int index : av.getColumnSelection().getSelected())
{
- anot[sel] = null;
+ if (av.getColumnSelection().isVisible(index))
+ {
+ anot[index] = null;
+ }
}
}
- else if (evt.getActionCommand().equals(LABEL))
+ else if (action.equals(LABEL))
{
String exMesg = collectAnnotVals(anot, LABEL);
String label = JOptionPane.showInputDialog(this,
if (anot[index] == null)
{
- anot[index] = new Annotation(label, "", ' ', 0); // TODO: verify that
- // null exceptions
- // aren't raised
- // elsewhere.
+ anot[index] = new Annotation(label, "", ' ', 0);
}
else
{
}
}
}
- else if (evt.getActionCommand().equals(COLOUR))
+ else if (action.equals(COLOUR))
{
Color col = JColorChooser.showDialog(this,
MessageManager.getString("label.select_foreground_colour"),
char type = 0;
String symbol = "\u03B1"; // alpha
- if (evt.getActionCommand().equals(HELIX))
+ if (action.equals(HELIX))
{
type = 'H';
}
- else if (evt.getActionCommand().equals(SHEET))
+ else if (action.equals(SHEET))
{
type = 'E';
symbol = "\u03B2"; // beta
}
// Added by LML to color stems
- else if (evt.getActionCommand().equals(STEM))
+ else if (action.equals(STEM))
{
type = 'S';
- symbol = "(";// "\u03C3"; // sigma
+ int column = av.getColumnSelection().getSelectedRanges().get(0)[0];
+ symbol = aa[activeRow].getDefaultRnaHelixSymbol(column);
}
if (!aa[activeRow].hasIcons)
aa[activeRow].hasIcons = true;
}
- symbol = getCurrentAnnotationCharacter(anot, symbol);
-
String label = JOptionPane.showInputDialog(MessageManager
.getString("label.enter_label_for_the_structure"), symbol);
if ((label.length() > 0) && !aa[activeRow].hasText)
{
aa[activeRow].hasText = true;
- if (evt.getActionCommand().equals(STEM))
+ if (action.equals(STEM))
{
aa[activeRow].showAllColLabels = true;
}
}
/**
- * Returns the current annotation symbol (if any) within the visible selected
- * columns (first symbol found left to right in selection). If none is found,
- * the supplied default value is returned.
+ * Returns any existing annotation concatenated as a string. For each
+ * annotation, takes the description, if any, else the secondary structure
+ * character (if type is HELIX, SHEET or STEM), else the display character (if
+ * type is LABEL).
*
- * @param annotations
- * @param defaultValue
+ * @param anots
+ * @param type
* @return
*/
- String getCurrentAnnotationCharacter(Annotation[] annotations,
- String defaultValue)
+ private String collectAnnotVals(Annotation[] anots, String type)
{
- String result = defaultValue;
- for (int index : av.getColumnSelection().getSelected())
- {
- if (!av.getColumnSelection().isVisible(index))
- {
- continue;
- }
+ // TODO is this method wanted? why? 'last' is not used
- Annotation annotation = annotations[index];
- if (annotation != null)
- {
- String displayed = annotation.displayCharacter;
- if (displayed != null && displayed.length() > 0)
- {
- result = displayed.substring(0, 1);
- break;
- }
- }
- }
- return result;
- }
-
- private String collectAnnotVals(Annotation[] anot, String label2)
- {
- String collatedInput = "";
+ StringBuilder collatedInput = new StringBuilder(64);
String last = "";
ColumnSelection viscols = av.getColumnSelection();
// TODO: refactor and save av.getColumnSelection for efficiency
- for (int index : viscols.getSelected())
+ List<Integer> selected = viscols.getSelected();
+ Collections.sort(selected);
+ for (int index : selected)
{
// always check for current display state - just in case
if (!viscols.isVisible(index))
continue;
}
String tlabel = null;
- if (anot[index] != null)
+ if (anots[index] != null)
{ // LML added stem code
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM) || label2.equals(LABEL))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM) || type.equals(LABEL))
{
- tlabel = anot[index].description;
+ tlabel = anots[index].description;
if (tlabel == null || tlabel.length() < 1)
{
- if (label2.equals(HELIX) || label2.equals(SHEET)
- || label2.equals(STEM))
+ if (type.equals(HELIX) || type.equals(SHEET)
+ || type.equals(STEM))
{
- tlabel = "" + anot[index].secondaryStructure;
+ tlabel = "" + anots[index].secondaryStructure;
}
else
{
- tlabel = "" + anot[index].displayCharacter;
+ tlabel = "" + anots[index].displayCharacter;
}
}
}
{
if (last.length() > 0)
{
- collatedInput += " ";
+ collatedInput.append(" ");
}
- collatedInput += tlabel;
+ collatedInput.append(tlabel);
}
}
}
- return collatedInput;
+ return collatedInput.toString();
}
/**
char residue = seqref.getCharAt(column);
if (!Comparison.isGap(residue))
{
+ text.append(" ");
+ String name;
+ if (av.getAlignment().isNucleotide())
+ {
+ name = ResidueProperties.nucleotideName.get(String
+ .valueOf(residue));
+ text.append(" Nucleotide: ").append(
+ name != null ? name : residue);
+ }
+ else
+ {
+ name = 'X' == residue ? "X" : ('*' == residue ? "STOP"
+ : ResidueProperties.aa2Triplet.get(String
+ .valueOf(residue)));
+ text.append(" Residue: ").append(name != null ? name : residue);
+ }
int residuePos = seqref.findPosition(column);
- text.append(": ").append(residue).append(" (")
- .append(residuePos).append(")");
+ text.append(" (").append(residuePos).append(")");
}
}
}
git://source.jalview.org / jalview.git / blobdiff