X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=bd903b34c4b6b386b176048dbd41af13221e4ff8;hb=3f12f4932226512316ec113e600695150431fd0a;hp=61a3f8caf1d65b897cfdfa227e4ea007867ba771;hpb=267f5674a53a735d8e13a2a4c12a4c8d8b0c1f00;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 61a3f8c..bd903b3 100755 --- 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.schemes.ResidueProperties; import jalview.util.Comparison; import jalview.util.MessageManager; @@ -48,6 +49,8 @@ import java.awt.event.MouseMotionListener; 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; @@ -290,9 +293,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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 (action.equals(LABEL)) @@ -422,13 +428,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - private String collectAnnotVals(Annotation[] anot, String label2) + /** + * 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 anots + * @param type + * @return + */ + private String collectAnnotVals(Annotation[] anots, String type) { - String collatedInput = ""; + // TODO is this method wanted? why? 'last' is not used + + 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 selected = viscols.getSelected(); + Collections.sort(selected); + for (int index : selected) { // always check for current display state - just in case if (!viscols.isVisible(index)) @@ -436,22 +456,22 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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; } } } @@ -459,13 +479,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { if (last.length() > 0) { - collatedInput += " "; + collatedInput.append(" "); } - collatedInput += tlabel; + collatedInput.append(tlabel); } } } - return collatedInput; + return collatedInput.toString(); } /** @@ -487,6 +507,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, int height = 0; activeRow = -1; + final int y = evt.getY(); for (int i = 0; i < aa.length; i++) { if (aa[i].visible) @@ -494,7 +515,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -504,58 +525,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { // Stretch Graph graphStretch = i; - graphStretchY = evt.getY(); + graphStretchY = y; } break; } } + /* + * isPopupTrigger fires in mousePressed on Mac, + * not until mouseRelease on Windows + */ if (evt.isPopupTrigger() && activeRow != -1) { - if (av.getColumnSelection() == null - || av.getColumnSelection().isEmpty()) - { - return; - } + showPopupMenu(y, evt.getX()); + return; + } - JPopupMenu pop = new JPopupMenu( - MessageManager.getString("label.structure_type")); - JMenuItem item; - /* - * Just display the needed structure options - */ - if (av.getAlignment().isNucleotide()) - { - item = new JMenuItem(STEM); - item.addActionListener(this); - pop.add(item); - } - else - { - item = new JMenuItem(HELIX); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(SHEET); - item.addActionListener(this); - pop.add(item); - } - item = new JMenuItem(LABEL); + ap.getScalePanel().mousePressed(evt); + } + + /** + * Construct and display a context menu at the right-click position + * + * @param y + * @param x + */ + void showPopupMenu(final int y, int x) + { + if (av.getColumnSelection() == null + || av.getColumnSelection().isEmpty()) + { + return; + } + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.structure_type")); + JMenuItem item; + /* + * Just display the needed structure options + */ + if (av.getAlignment().isNucleotide()) + { + item = new JMenuItem(STEM); item.addActionListener(this); pop.add(item); - item = new JMenuItem(COLOUR); + } + else + { + item = new JMenuItem(HELIX); item.addActionListener(this); pop.add(item); - item = new JMenuItem(REMOVE); + item = new JMenuItem(SHEET); item.addActionListener(this); pop.add(item); - pop.show(this, evt.getX(), evt.getY()); - - return; } - - ap.getScalePanel().mousePressed(evt); - + item = new JMenuItem(LABEL); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(COLOUR); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(REMOVE); + item.addActionListener(this); + pop.add(item); + pop.show(this, x, y); } /** @@ -571,6 +605,16 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, graphStretchY = -1; mouseDragging = false; ap.getScalePanel().mouseReleased(evt); + + /* + * isPopupTrigger is set in mouseReleased on Windows + * (in mousePressed on Mac) + */ + if (evt.isPopupTrigger() && activeRow != -1) + { + showPopupMenu(evt.getY(), evt.getX()); + } + } /** @@ -775,9 +819,24 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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(")"); } } }