X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=919356f28f3064e6cc57031a3c2fb8cb37068dd9;hb=1ec8fc3e8bc982115e5ba1b16a101d239a2df591;hp=3c9a13eecbcedb347af210a3bc06d084ff3f1c09;hpb=45694fc1af8ff3cad6cb50331577403fa670d502;p=jalview.git diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java index 3c9a13e..919356f 100755 --- a/src/jalview/gui/AnnotationPanel.java +++ b/src/jalview/gui/AnnotationPanel.java @@ -23,6 +23,7 @@ package jalview.gui; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SequenceI; import jalview.renderer.AnnotationRenderer; import jalview.renderer.AwtRenderPanelI; @@ -49,12 +50,12 @@ 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; @@ -122,8 +123,6 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, boolean mouseDragging = false; - boolean MAC = false; - // for editing cursor int cursorX = 0; @@ -141,9 +140,6 @@ 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); @@ -290,20 +286,21 @@ 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 index : av.getColumnSelection().getSelected()) { - if (av.getColumnSelection().isVisible(index)) + if (av.getAlignment().getHiddenColumns().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) @@ -318,17 +315,14 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, for (int index : av.getColumnSelection().getSelected()) { - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) { continue; } 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 { @@ -336,7 +330,7 @@ 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"), @@ -344,7 +338,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, for (int index : av.getColumnSelection().getSelected()) { - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) { continue; } @@ -361,23 +355,24 @@ 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) @@ -385,7 +380,7 @@ 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) @@ -396,14 +391,14 @@ 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 index : av.getColumnSelection().getSelected()) { - if (!av.getColumnSelection().isVisible(index)) + if (!av.getAlignment().getHiddenColumns().isVisible(index)) { continue; } @@ -446,21 +441,26 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, StringBuilder collatedInput = new StringBuilder(64); String last = ""; ColumnSelection viscols = av.getColumnSelection(); - // TODO: refactor and save av.getColumnSelection for efficiency - List selected = viscols.getSelected(); + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + + /* + * 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)) + if (!hidden.isVisible(index)) { continue; } String tlabel = null; if (anots[index] != null) { // LML added stem code - if (type.equals(HELIX) || type.equals(SHEET) - || type.equals(STEM) || type.equals(LABEL)) + if (type.equals(HELIX) || type.equals(SHEET) || type.equals(STEM) + || type.equals(LABEL)) { tlabel = anots[index].description; if (tlabel == null || tlabel.length() < 1) @@ -508,6 +508,7 @@ 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) @@ -515,7 +516,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI, height += aa[i].height; } - if (evt.getY() < height) + if (y < height) { if (aa[i].editable) { @@ -525,62 +526,71 @@ 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); } /** @@ -596,6 +606,16 @@ 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()); + } + } /** @@ -689,11 +709,13 @@ 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()) { - column = av.getColumnSelection().adjustForHiddenColumns(column); + column = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(column); } AlignmentAnnotation ann = aa[row]; @@ -795,8 +817,7 @@ 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)) { @@ -887,7 +908,8 @@ 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; @@ -928,7 +950,8 @@ 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); } @@ -958,8 +981,8 @@ 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 @@ -1115,4 +1138,25 @@ 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(); + } + } }