X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=84f3e6c56925862ad035d072827b838b98c3a074;hb=9eabd6dffd6d19b2826b887a5def80351b9bceed;hp=398f57d0fcb9a1b975beea3a0fe41965878f4cd7;hpb=076e8c3064e29c735041c84abb792e60fa9522e5;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 398f57d..84f3e6c 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; @@ -48,10 +49,12 @@ import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.awt.image.BufferedImage; +import java.util.ArrayList; +import java.util.Collections; +import java.util.List; import javax.swing.JColorChooser; import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.Scrollable; @@ -119,8 +122,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, boolean mouseDragging = false; - boolean MAC = false; - // for editing cursor int cursorX = 0; @@ -138,9 +139,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public AnnotationPanel(AlignmentPanel ap) { - - MAC = jalview.util.Platform.isAMac(); - ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -287,17 +285,21 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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, + String label = JvOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"), exMesg); if (label == null) @@ -319,10 +321,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, 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 { @@ -330,7 +329,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } } - else if (evt.getActionCommand().equals(COLOUR)) + else if (action.equals(COLOUR)) { Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_foreground_colour"), @@ -355,23 +354,24 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, // HELIX, SHEET or STEM { char type = 0; - String symbol = "\u03B1"; + 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"; + symbol = "\u03B2"; // beta } // Added by LML to color stems - else if (evt.getActionCommand().equals(STEM)) + else if (action.equals(STEM)) { type = 'S'; - symbol = "\u03C3"; + int column = av.getColumnSelection().getSelectedRanges().get(0)[0]; + symbol = aa[activeRow].getDefaultRnaHelixSymbol(column); } if (!aa[activeRow].hasIcons) @@ -379,7 +379,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasIcons = true; } - String label = JOptionPane.showInputDialog(MessageManager + String label = JvOptionPane.showInputDialog(MessageManager .getString("label.enter_label_for_the_structure"), symbol); if (label == null) @@ -390,7 +390,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if ((label.length() > 0) && !aa[activeRow].hasText) { aa[activeRow].hasText = true; - if (evt.getActionCommand().equals(STEM)) + if (action.equals(STEM)) { aa[activeRow].showAllColLabels = true; } @@ -423,13 +423,31 @@ 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()) + + /* + * the selection list (read-only view) is in selection order, not + * column order; make a copy so we can sort it + */ + List selected = new ArrayList(viscols.getSelected()); + Collections.sort(selected); + for (int index : selected) { // always check for current display state - just in case if (!viscols.isVisible(index)) @@ -437,22 +455,22 @@ 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; } } } @@ -460,13 +478,13 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { if (last.length() > 0) { - collatedInput += " "; + collatedInput.append(" "); } - collatedInput += tlabel; + collatedInput.append(tlabel); } } } - return collatedInput; + return collatedInput.toString(); } /** @@ -488,6 +506,7 @@ 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) @@ -495,7 +514,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -505,62 +524,71 @@ 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) - { - 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() == true) - { - 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; } - - if (aa == null) - { - 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); } /** @@ -576,6 +604,16 @@ 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()); + } + } /** @@ -669,7 +707,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } - int column = (evt.getX() / av.getCharWidth()) + av.getStartRes(); + int column = (evt.getX() / av.getCharWidth()) + + av.getRanges().getStartRes(); if (av.hasHiddenColumns()) { @@ -775,14 +814,28 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { text.append(", ") .append(MessageManager.getString("label.sequence")) - .append(" ") - .append(seqIndex + 1); + .append(" ").append(seqIndex + 1); 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(")"); } } } @@ -852,7 +905,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } } - imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth(); + imgWidth = (av.getRanges().getEndRes() - av.getRanges().getStartRes() + 1) + * av.getCharWidth(); if (imgWidth < 1) { return; @@ -893,7 +947,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, imageFresh = true; } - drawComponent(gg, av.startRes, av.endRes + 1); + drawComponent(gg, av.getRanges().getStartRes(), av.getRanges() + .getEndRes() + 1); imageFresh = false; g.drawImage(image, 0, 0, this); } @@ -923,8 +978,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.getCharWidth(), 0); long mtime = System.currentTimeMillis(); - int sr = av.startRes; - int er = av.endRes + 1; + int sr = av.getRanges().getStartRes(); + int er = av.getRanges().getEndRes() + 1; int transX = 0; if (horizontal > 0) // scrollbar pulled right, image to the left @@ -1080,4 +1135,25 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return null; } } + + /** + * Try to ensure any references held are nulled + */ + public void dispose() + { + av = null; + ap = null; + image = null; + fadedImage = null; + gg = null; + _mwl = null; + + /* + * I created the renderer so I will dispose of it + */ + if (renderer != null) + { + renderer.dispose(); + } + } }