X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=db3cb8c2837c28018dce334d8fddacec76b7e958;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=b2f73ed0167978aa9789c9a9875a92c6bcfff25a;hpb=86e5fb244905902a1ba1a2d732a0d5bebdb1de39;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index b2f73ed..db3cb8c 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -24,7 +24,8 @@ import java.awt.event.*; import jalview.datamodel.*; -public class AlignmentPanel extends Panel implements AdjustmentListener +public class AlignmentPanel + extends Panel implements AdjustmentListener { AlignViewport av; @@ -40,18 +41,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // this value is set false when selection area being dragged boolean fastPaint = true; - boolean MAC = false; - public AlignmentPanel(AlignFrame af, final AlignViewport av) { - this.addKeyListener(new KeyAdapter() - { - public void keyPressed(KeyEvent ke) - { - System.out.println("Align Panel "+ke); - } - }); - try { jbInit(); @@ -61,9 +52,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener e.printStackTrace(); } - if(System.getProperty("os.name").startsWith("Mac")) - MAC = true; - alignFrame = af; this.av = av; seqPanel = new SeqPanel(av, this); @@ -71,11 +59,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener scalePanel = new ScalePanel(av, this); idwidthAdjuster = new IdwidthAdjuster(this); annotationPanel = new AnnotationPanel(this); + + sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH); + alabels = new AnnotationLabels(this); + setAnnotationVisible(av.showAnnotation); + idPanelHolder.add(idPanel, BorderLayout.CENTER); idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); - annotationScroller.add(annotationPanel); annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); scalePanelHolder.add(scalePanel, BorderLayout.CENTER); seqPanelHolder.add(seqPanel, BorderLayout.CENTER); @@ -99,36 +91,70 @@ public class AlignmentPanel extends Panel implements AdjustmentListener idPanel.idCanvas.setSize(d); hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height); - annotationScroller.setSize(annotationPanel.getSize()); idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); annotationSpaceFillerHolder.setSize(d.width, annotationPanel.getSize().height); alabels.setSize(d.width, annotationPanel.getSize().height); + final AlignmentPanel ap = this; + av.addPropertyChangeListener(new java.beans.PropertyChangeListener() + { + public void propertyChange(java.beans.PropertyChangeEvent evt) + { + if (evt.getPropertyName().equals("alignment")) + { + PaintRefresher.Refresh(ap, + av.getSequenceSetId(), + true, + true); + alignmentChanged(); + } + } + }); + } + public void alignmentChanged() + { + av.alignmentChanged(this); + + if (overviewPanel != null) + { + overviewPanel.updateOverviewImage(); + } + + alignFrame.updateEditMenuBar(); + + repaint(); + } public void fontChanged() { // set idCanvas bufferedImage to null // to prevent drawing old image + idPanel.idCanvas.image = null; FontMetrics fm = getFontMetrics(av.getFont()); scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent())); idwidthAdjuster.setSize(new Dimension(10, av.charHeight + fm.getDescent())); - annotationPanel.adjustPanelHeight(); + annotationPanel.image = null; + int ap = annotationPanel.adjustPanelHeight(); annotationPanel.repaint(); Dimension d = calculateIdWidth(); d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height); + alabels.setSize(d.width + 4, ap); idPanel.idCanvas.setSize(d); hscrollFillerPanel.setSize(d); - alignFrame.pack(); + validate(); + repaint(); - if(overviewPanel!=null) - overviewPanel.updateOverviewImage(); + if (overviewPanel != null) + { + overviewPanel.updateOverviewImage(); + } } public void setIdWidth(int w, int h) @@ -141,16 +167,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener Dimension calculateIdWidth() { - Frame frame = new Frame(); - frame.addNotify(); - Graphics g = frame.getGraphics(); - if (g == null) + if (av.nullFrame == null) { - Frame f = new Frame(); - f.addNotify(); - g = f.getGraphics(); + av.nullFrame = new Frame(); + av.nullFrame.addNotify(); } + Graphics g = av.nullFrame.getGraphics(); + FontMetrics fm = g.getFontMetrics(av.font); AlignmentI al = av.getAlignment(); @@ -173,7 +197,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener i = 0; if (al.getAlignmentAnnotation() != null) { - fm = g.getFontMetrics(frame.getFont()); + fm = g.getFontMetrics(av.nullFrame.getFont()); while (i < al.getAlignmentAnnotation().length) { String label = al.getAlignmentAnnotation()[i].label; @@ -188,25 +212,60 @@ public class AlignmentPanel extends Panel implements AdjustmentListener return new Dimension(idWidth, idPanel.idCanvas.getSize().height); } - public void highlightSearchResults(int[] results) + public void highlightSearchResults(SearchResults results) { seqPanel.seqCanvas.highlightSearchResults(results); // do we need to scroll the panel? if (results != null) { - SequenceI seq = av.alignment.getSequenceAt(results[0]); - int start = seq.findIndex(results[1]) - 1; - int end = seq.findIndex(results[2]) - 1; - if (av.getStartRes() > start - || av.getEndRes() < end - || (av.getStartSeq() > results[0] - || av.getEndSeq() < results[0])) + SequenceI seq = results.getResultSequence(0); + int seqIndex = av.alignment.findIndex(seq); + int start = seq.findIndex(results.getResultStart(0)) - 1; + int end = seq.findIndex(results.getResultEnd(0)) - 1; + + if (!av.wrapAlignment) + { + if ( (av.getStartRes() > end) || (av.getEndRes() < start) || + ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + { + if (start > av.alignment.getWidth() - hextent) + { + start = av.alignment.getWidth() - hextent; + if (start < 0) + { + start = 0; + } + } + if (seqIndex > av.alignment.getHeight() - vextent) + { + seqIndex = av.alignment.getHeight() - vextent; + if (seqIndex < 0) + { + seqIndex = 0; + } + } + setScrollValues(start, seqIndex); + } + } + else { - setScrollValues(start, results[0]); + scrollToWrappedVisible(start); } } + repaint(); + } + + void scrollToWrappedVisible(int res) + { + int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas. + getSize().width); + if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth)) + { + vscroll.setValue(res / cwidth); + av.startRes = vscroll.getValue() * cwidth; + } } public OverviewPanel getOverviewPanel() @@ -224,7 +283,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); + annotationPanel.setVisible(b); } validate(); repaint(); @@ -233,29 +292,32 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public void setWrapAlignment(boolean wrap) { av.startSeq = 0; + av.startRes = 0; scalePanelHolder.setVisible(!wrap); + hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); if (wrap) { - annotationScroller.setVisible(false); + annotationPanel.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.showAnnotation) { - annotationScroller.setVisible(true); + annotationPanel.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } idSpaceFillerPanel1.setVisible(!wrap); + fontChanged(); //This is so that the scalePanel is resized correctly + validate(); repaint(); } - int hextent = 0; int vextent = 0; @@ -268,8 +330,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); + setScrollValues(hscroll.getValue(), vscroll.getValue() - 1); } else { @@ -277,24 +338,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); + setScrollValues(hscroll.getValue(), vscroll.getValue() + 1); } - fastPaint = true; + + repaint(); return true; } public boolean scrollRight(boolean right) { - - if (right) + if (!right) { if (hscroll.getValue() < 1) { return false; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); + setScrollValues(hscroll.getValue() - 1, vscroll.getValue()); } else { @@ -302,40 +361,47 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { return false; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); + setScrollValues(hscroll.getValue() + 1, vscroll.getValue()); } - fastPaint = true; + + repaint(); return true; } public void setScrollValues(int x, int y) { + int width = av.alignment.getWidth(); + int height = av.alignment.getHeight(); + + if (av.hasHiddenColumns) + { + width = av.getColumnSelection().findColumnPosition(width); + } av.setStartRes(x); - av.setStartSeq(y); - av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1); + av.setEndRes( (x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; - if (hextent > av.alignment.getWidth()) + if (hextent > width) { - hextent = av.alignment.getWidth(); + hextent = width; } - if (vextent > av.alignment.getHeight()) + + if (vextent > height) { - vextent = av.alignment.getHeight(); + vextent = height; } - if (hextent + x > av.getAlignment().getWidth()) + if ( (hextent + x) > width) { - x = av.getAlignment().getWidth() - hextent; + x = width - hextent; } - if (vextent + y > av.getAlignment().getHeight()) + if ( (vextent + y) > height) { - y = av.getAlignment().getHeight() - vextent; + y = height - vextent; } if (y < 0) @@ -348,6 +414,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener x = 0; } + av.setStartSeq(y); + int endSeq = y + vextent; if (endSeq > av.alignment.getHeight()) { @@ -355,8 +423,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener } av.setEndSeq(endSeq); - hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); - vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + + if (overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } } @@ -365,7 +438,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener int oldX = av.getStartRes(); int oldY = av.getStartSeq(); - if (evt.getSource() == hscroll) + if (evt == null || evt.getSource() == hscroll) { int x = hscroll.getValue(); av.setStartRes(x); @@ -373,7 +446,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 1); } - if (evt.getSource() == vscroll) + if (evt == null || evt.getSource() == vscroll) { int offy = vscroll.getValue(); if (av.getWrapAlignment()) @@ -396,15 +469,29 @@ public class AlignmentPanel extends Panel implements AdjustmentListener overviewPanel.setBoxPosition(); } - if (av.getWrapAlignment() || !fastPaint || MAC) + int scrollX = av.startRes - oldX; + int scrollY = av.startSeq - oldY; + + if (av.getWrapAlignment() || !fastPaint || av.MAC) { repaint(); } else { - idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); - seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX, - av.getStartSeq() - oldY); + // Make sure we're not trying to draw a panel + // larger than the visible window + if (scrollX > av.endRes - av.startRes) + { + scrollX = av.endRes - av.startRes; + } + else if (scrollX < av.startRes - av.endRes) + { + scrollX = av.startRes - av.endRes; + } + + idPanel.idCanvas.fastPaint(scrollY); + seqPanel.seqCanvas.fastPaint(scrollX, + scrollY); scalePanel.repaint(); if (av.getShowAnnotation()) @@ -422,6 +509,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public void paint(Graphics g) { + invalidate(); Dimension d = idPanel.idCanvas.getSize(); idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); annotationSpaceFillerHolder.setSize(d.width, @@ -431,12 +519,23 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (av.getWrapAlignment()) { - int max = av.alignment.getWidth() / - seqPanel.seqCanvas. - getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width) +1; - vscroll.setMaximum(max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); + int maxwidth = av.alignment.getWidth(); + + if (av.hasHiddenColumns) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth + (seqPanel.seqCanvas.getSize().width); + + if (canvasWidth > 0) + { + int max = maxwidth / canvasWidth; + vscroll.setMaximum(max); + vscroll.setUnitIncrement(1); + vscroll.setVisibleAmount(1); + } } else { @@ -453,7 +552,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (getBounds() == g.getClipBounds()) { if (overviewPanel != null) + { overviewPanel.updateOverviewImage(); + } } } @@ -475,55 +576,54 @@ public class AlignmentPanel extends Panel implements AdjustmentListener BorderLayout borderLayout10 = new BorderLayout(); protected Panel hscrollFillerPanel = new Panel(); BorderLayout borderLayout11 = new BorderLayout(); - public Panel annotationScroller = new Panel(); BorderLayout borderLayout4 = new BorderLayout(); BorderLayout borderLayout2 = new BorderLayout(); - private void jbInit() throws Exception { - // idPanelHolder.setPreferredSize(new Dimension(70, 10)); - this.setLayout(borderLayout7); - - // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); - sequenceHolderPanel.setLayout(borderLayout3); - seqPanelHolder.setLayout(borderLayout1); - scalePanelHolder.setBackground(Color.white); - - // scalePanelHolder.setPreferredSize(new Dimension(10, 30)); - scalePanelHolder.setLayout(borderLayout6); - idPanelHolder.setLayout(borderLayout5); - idSpaceFillerPanel1.setBackground(Color.white); - - // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30)); - idSpaceFillerPanel1.setLayout(borderLayout11); - annotationSpaceFillerHolder.setBackground(Color.white); - - // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80)); - annotationSpaceFillerHolder.setLayout(borderLayout4); - hscroll.setOrientation(Scrollbar.HORIZONTAL); - hscrollHolder.setLayout(borderLayout10); - hscrollFillerPanel.setBackground(Color.white); - - // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10)); - hscrollHolder.setBackground(Color.white); - - // annotationScroller.setPreferredSize(new Dimension(10, 80)); - // this.setPreferredSize(new Dimension(220, 166)); - seqPanelHolder.setBackground(Color.white); - idPanelHolder.setBackground(Color.white); - annotationScroller.setLayout(borderLayout2); - sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH); - sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER); - seqPanelHolder.add(vscroll, BorderLayout.EAST); - sequenceHolderPanel.add(annotationScroller, BorderLayout.SOUTH); - - // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH); - this.add(idPanelHolder, BorderLayout.WEST); - idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH); - idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH); - this.add(hscrollHolder, BorderLayout.SOUTH); - hscrollHolder.add(hscroll, BorderLayout.CENTER); - hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST); - this.add(sequenceHolderPanel, BorderLayout.CENTER); + private void jbInit() + throws Exception + { + // idPanelHolder.setPreferredSize(new Dimension(70, 10)); + this.setLayout(borderLayout7); + + // sequenceHolderPanel.setPreferredSize(new Dimension(150, 150)); + sequenceHolderPanel.setLayout(borderLayout3); + seqPanelHolder.setLayout(borderLayout1); + scalePanelHolder.setBackground(Color.white); + + // scalePanelHolder.setPreferredSize(new Dimension(10, 30)); + scalePanelHolder.setLayout(borderLayout6); + idPanelHolder.setLayout(borderLayout5); + idSpaceFillerPanel1.setBackground(Color.white); + + // idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30)); + idSpaceFillerPanel1.setLayout(borderLayout11); + annotationSpaceFillerHolder.setBackground(Color.white); + + // annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80)); + annotationSpaceFillerHolder.setLayout(borderLayout4); + hscroll.setOrientation(Scrollbar.HORIZONTAL); + hscrollHolder.setLayout(borderLayout10); + hscrollFillerPanel.setBackground(Color.white); + + // hscrollFillerPanel.setPreferredSize(new Dimension(70, 10)); + hscrollHolder.setBackground(Color.white); + + // annotationScroller.setPreferredSize(new Dimension(10, 80)); + // this.setPreferredSize(new Dimension(220, 166)); + seqPanelHolder.setBackground(Color.white); + idPanelHolder.setBackground(Color.white); + sequenceHolderPanel.add(scalePanelHolder, BorderLayout.NORTH); + sequenceHolderPanel.add(seqPanelHolder, BorderLayout.CENTER); + seqPanelHolder.add(vscroll, BorderLayout.EAST); + + // Panel3.add(secondaryPanelHolder, BorderLayout.SOUTH); + this.add(idPanelHolder, BorderLayout.WEST); + idPanelHolder.add(idSpaceFillerPanel1, BorderLayout.NORTH); + idPanelHolder.add(annotationSpaceFillerHolder, BorderLayout.SOUTH); + this.add(hscrollHolder, BorderLayout.SOUTH); + hscrollHolder.add(hscroll, BorderLayout.CENTER); + hscrollHolder.add(hscrollFillerPanel, BorderLayout.WEST); + this.add(sequenceHolderPanel, BorderLayout.CENTER); } }