X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=199c4e599a9ff1e5cc0cf83a272f668e993b91b1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=e5bed74ed72292dd7276cfdf2bb7a207591681d0;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index e5bed74..199c4e5 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -26,6 +26,8 @@ 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; import java.awt.AlphaComposite; @@ -47,6 +49,9 @@ 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; @@ -54,7 +59,6 @@ import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JPopupMenu; import javax.swing.Scrollable; -import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** @@ -119,8 +123,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, boolean mouseDragging = false; - boolean MAC = false; - // for editing cursor int cursorX = 0; @@ -138,9 +140,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, */ public AnnotationPanel(AlignmentPanel ap) { - - MAC = new jalview.util.Platform().isAMac(); - ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -287,16 +286,20 @@ 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 i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - anot[av.getColumnSelection().columnAt(i)] = null; + if (av.getColumnSelection().isVisible(index)) + { + anot[index] = null; + } } } - else if (evt.getActionCommand().equals(LABEL)) + else if (action.equals(LABEL)) { - String exMesg = collectAnnotVals(anot, av.getColumnSelection(), LABEL); + String exMesg = collectAnnotVals(anot, LABEL); String label = JOptionPane.showInputDialog(this, MessageManager.getString("label.enter_label"), exMesg); @@ -310,10 +313,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, aa[activeRow].hasText = true; } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - if (!av.getColumnSelection().isVisible(index)) { continue; @@ -321,10 +322,7 @@ 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 { @@ -332,15 +330,14 @@ 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"), Color.black); + MessageManager.getString("label.select_foreground_colour"), + Color.black); - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - if (!av.getColumnSelection().isVisible(index)) { continue; @@ -355,26 +352,27 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } } else - // HELIX OR SHEET + // 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) @@ -393,15 +391,13 @@ 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; } } - for (int i = 0; i < av.getColumnSelection().size(); i++) + for (int index : av.getColumnSelection().getSelected()) { - int index = av.getColumnSelection().columnAt(i); - if (!av.getColumnSelection().isVisible(index)) { continue; @@ -412,54 +408,70 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, anot[index] = new Annotation(label, "", type, 0); } - anot[index].secondaryStructure = type != 'S' ? type : label .length() == 0 ? ' ' : label.charAt(0); anot[index].displayCharacter = label; } } + av.getAlignment().validateAnnotation(aa[activeRow]); ap.alignmentChanged(); - + ap.alignFrame.setMenusForViewport(); adjustPanelHeight(); repaint(); return; } - private String collectAnnotVals(Annotation[] anot, - ColumnSelection columnSelection, 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 i = 0; i < columnSelection.size(); i++) + + /* + * 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) { - int index = columnSelection.columnAt(i); // 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; } } } @@ -467,13 +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(); } /** @@ -495,6 +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) @@ -502,7 +515,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -512,62 +525,71 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { // Stretch Graph graphStretch = i; - graphStretchY = evt.getY(); + graphStretchY = y; } break; } } - if (SwingUtilities.isRightMouseButton(evt) && activeRow != -1) + /* + * 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); } /** @@ -583,6 +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()); + } + } /** @@ -637,10 +669,10 @@ 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) @@ -666,7 +698,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (evt.getY() < height) { row = i; - break; } } @@ -677,64 +708,139 @@ 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(""); + for (int i = 0; i < anns.length; i++) { - StringBuffer tip = new StringBuffer(""); - 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 + "
"); + tip.append(" ").append(description); } - } - if (tip.length() != 6) - { - tip.setLength(tip.length() - 4); - this.setToolTipText(tip.toString() + ""); + tip.append("
"); } } - 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() + ""); } - 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); + 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(residuePos).append(")"); } - - ap.alignFrame.statusBar.setText(text.toString()); } } - else - { - this.setToolTipText(null); - } + + ap.alignFrame.statusBar.setText(text.toString()); } /** @@ -757,10 +863,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, public void drawCursor(Graphics graphics, SequenceI seq, int res, int x1, int y1) { - int pady = av.charHeight / 5; + int pady = av.getCharHeight() / 5; int charOffset = 0; graphics.setColor(Color.black); - graphics.fillRect(x1, y1, av.charWidth, av.charHeight); + graphics.fillRect(x1, y1, av.getCharWidth(), av.getCharHeight()); if (av.validCharWidth) { @@ -768,9 +874,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, char s = seq.getCharAt(res); - charOffset = (av.charWidth - fm.charWidth(s)) / 2; + charOffset = (av.getCharWidth() - fm.charWidth(s)) / 2; graphics.drawString(String.valueOf(s), charOffset + x1, - (y1 + av.charHeight) - pady); + (y1 + av.getCharHeight()) - pady); } } @@ -799,7 +905,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } } - imgWidth = (av.endRes - av.startRes + 1) * av.charWidth; + imgWidth = (av.endRes - av.startRes + 1) * av.getCharWidth(); if (imgWidth < 1) { return; @@ -809,8 +915,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, { try { - image = new BufferedImage(imgWidth, ap.getAnnotationPanel().getHeight(), - BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(imgWidth, ap.getAnnotationPanel() + .getHeight(), BufferedImage.TYPE_INT_RGB); } catch (OutOfMemoryError oom) { try @@ -867,7 +973,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, return; } long stime = System.currentTimeMillis(); - gg.copyArea(0, 0, imgWidth, getHeight(), -horizontal * av.charWidth, 0); + gg.copyArea(0, 0, imgWidth, getHeight(), + -horizontal * av.getCharWidth(), 0); long mtime = System.currentTimeMillis(); int sr = av.startRes; int er = av.endRes + 1; @@ -875,7 +982,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, if (horizontal > 0) // scrollbar pulled right, image to the left { - transX = (er - sr - horizontal) * av.charWidth; + transX = (er - sr - horizontal) * av.getCharWidth(); sr = er - horizontal; } else if (horizontal < 0) @@ -960,7 +1067,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, } g.setColor(Color.white); - g.fillRect(0, 0, (endRes - startRes) * av.charWidth, getHeight()); + g.fillRect(0, 0, (endRes - startRes) * av.getCharWidth(), getHeight()); g.setFont(av.getFont()); if (fm == null) @@ -1026,4 +1133,25 @@ 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(); + } + } }