X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=874b552f443310726d10179c9ed99ad066cdd68b;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=5e09da79a02e66e6db05fec25a2b206e0c5c14dc;hpb=3402d066dbd7667cd805e6d78ac5eca66e237c72;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java index 5e09da7..874b552 100755 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,508 +1,691 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -package jalview.appletgui; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.jbappletgui.*; -import jalview.schemes.*; - -public class AlignmentPanel - extends GAlignmentPanel implements AdjustmentListener -{ - - AlignViewport av; - OverviewPanel overviewPanel; - SeqPanel seqPanel; - IdPanel idPanel; - IdwidthAdjuster idwidthAdjuster; - public AlignFrame alignFrame; - ScalePanel scalePanel; - AnnotationPanel annotationPanel; - AnnotationLabels alabels; - - // this value is set false when selection area being dragged - boolean fastPaint = true; - - public AlignmentPanel(AlignFrame af, final AlignViewport av) - { - alignFrame = af; - this.av = av; - seqPanel = new SeqPanel(av, this); - idPanel = new IdPanel(av, this); - scalePanel = new ScalePanel(av, this); - idwidthAdjuster = new IdwidthAdjuster(this); - annotationPanel = new AnnotationPanel(this); - alabels = new AnnotationLabels(this); - - 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); - - fontChanged(); - setScrollValues(0, 0); - - hscroll.addAdjustmentListener(this); - vscroll.addAdjustmentListener(this); - - seqPanel.seqCanvas.addKeyListener(new MyKeyAdapter()); - idPanel.idCanvas.addKeyListener(new MyKeyAdapter()); - - addComponentListener(new ComponentAdapter() - { - public void componentResized(ComponentEvent evt) - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - repaint(); - } - }); - - Dimension d = calculateIdWidth(); - 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); - - } - - class MyKeyAdapter - extends KeyAdapter - { - public void keyPressed(KeyEvent evt) - { - // System.out.println(evt.getKeyCode()); log. - switch (evt.getKeyCode()) - { - case 27: // escape key - av.setSelectionGroup(null); - alignFrame.alignPanel.repaint(); - break; - case KeyEvent.VK_X: - if (evt.isControlDown()) - { - alignFrame.cut_actionPerformed(null); - } - break; - case KeyEvent.VK_C: - if (evt.isControlDown()) - { - alignFrame.copy_actionPerformed(null); - } - break; - case KeyEvent.VK_V: - if (evt.isControlDown()) - { - alignFrame.paste(true); - } - break; - case KeyEvent.VK_A: - if (evt.isControlDown()) - { - alignFrame.selectAllSequenceMenuItem_actionPerformed(null); - } - break; - case KeyEvent.VK_DOWN: - alignFrame.moveSelectedSequences(false); - break; - case KeyEvent.VK_UP: - alignFrame.moveSelectedSequences(true); - break; - case KeyEvent.VK_F: - if (evt.isControlDown()) - { - alignFrame.findMenuItem_actionPerformed(null); - } - break; - case KeyEvent.VK_BACK_SPACE: - case KeyEvent.VK_DELETE: - alignFrame.cut_actionPerformed(null); - break; - - } - } - } - - public void fontChanged() - { - // set idCanvas bufferedImage to null - // to prevent drawing old image - 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.repaint(); - Dimension d = calculateIdWidth(); - d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height); - idPanel.idCanvas.setSize(d); - hscrollFillerPanel.setSize(d); - - alignFrame.pack(); - } - - public void setIdWidth(int w, int h) - { - idPanel.idCanvas.setSize(w, h); - idPanelHolder.setSize(w, idPanelHolder.getSize().height); - alabels.setSize(w, alabels.getSize().height); - validate(); - } - - Dimension calculateIdWidth() - { - Frame frame = new Frame(); - frame.addNotify(); - Graphics g = frame.getGraphics(); - if (g == null) - { - Frame f = new Frame(); - f.addNotify(); - g = f.getGraphics(); - } - - FontMetrics fm = g.getFontMetrics(av.font); - AlignmentI al = av.getAlignment(); - - int i = 0; - int idWidth = 0; - String id; - while (i < al.getHeight() && al.getSequenceAt(i) != null) - { - SequenceI s = al.getSequenceAt(i); - if (av.getShowFullId()) - { - id = s.getDisplayId(); - } - else - { - id = s.getName(); - } - - if (fm.stringWidth(id) > idWidth) - { - idWidth = fm.stringWidth(id); - } - i++; - } - - // Also check annotation label widths - i = 0; - if (al.getAlignmentAnnotation() != null) - { - fm = g.getFontMetrics(frame.getFont()); - while (i < al.getAlignmentAnnotation().length) - { - String label = al.getAlignmentAnnotation()[i].label; - if (fm.stringWidth(label) > idWidth) - { - idWidth = fm.stringWidth(label); - } - i++; - } - } - - return new Dimension(idWidth, idPanel.idCanvas.getSize().height); - } - - public void highlightSearchResults(int[] 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])) - { - setScrollValues(start, results[0]); - } - } - - } - - public OverviewPanel getOverviewPanel() - { - return overviewPanel; - } - - public void setOverviewPanel(OverviewPanel op) - { - overviewPanel = op; - } - - public void setAnnotationVisible(boolean b) - { - annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); - validate(); - repaint(); - } - - public void setWrapAlignment(boolean wrap) - { - scalePanelHolder.setVisible(!wrap); - hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); - - av.setShowAnnotation(!wrap); - annotationScroller.setVisible(!wrap); - annotationSpaceFillerHolder.setVisible(!wrap); - idSpaceFillerPanel1.setVisible(!wrap); - - validate(); - repaint(); - - } - - public void setColourScheme() - { - ColourSchemeI cs = av.getGlobalColourScheme(); - - if (av.getConservationSelected()) - { - - Alignment al = (Alignment) av.getAlignment(); - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth()); - - c.calculate(); - c.verdict(false, av.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, cs); - - av.setGlobalColourScheme(ccs); - - } - - repaint(); - } - - int hextent = 0; - int vextent = 0; - - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) - { - if (up) - { - if (vscroll.getValue() < 1) - { - return false; - } - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); - } - else - { - if (vextent + vscroll.getValue() >= av.getAlignment().getHeight()) - { - return false; - } - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); - } - fastPaint = true; - return true; - } - - public boolean scrollRight(boolean right) - { - - if (right) - { - if (hscroll.getValue() < 1) - { - return false; - } - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); - } - else - { - if (hextent + hscroll.getValue() >= av.getAlignment().getWidth()) - { - return false; - } - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); - } - fastPaint = true; - return true; - } - - public void setScrollValues(int x, int y) - { - - av.setStartRes(x); - av.setStartSeq(y); - av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - 1); - - hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; - vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; - - if (hextent > av.alignment.getWidth()) - { - hextent = av.alignment.getWidth(); - } - if (vextent > av.alignment.getHeight()) - { - vextent = av.alignment.getHeight(); - } - - if (hextent + x > av.getAlignment().getWidth()) - { - x = av.getAlignment().getWidth() - hextent; - } - - if (vextent + y > av.getAlignment().getHeight()) - { - y = av.getAlignment().getHeight() - vextent; - } - - if (y < 0) - { - y = 0; - } - - if (x < 0) - { - x = 0; - } - - int endSeq = y + vextent; - if (endSeq > av.alignment.getHeight()) - { - endSeq = av.alignment.getHeight(); - } - - av.setEndSeq(endSeq); - hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth()); - vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight()); - - } - - public void adjustmentValueChanged(AdjustmentEvent evt) - { - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); - - if (evt.getSource() == hscroll) - { - int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes(x + seqPanel.seqCanvas.getSize().width / av.getCharWidth() - - 1); - } - - if (evt.getSource() == vscroll) - { - int offy = vscroll.getValue(); - if (av.getWrapAlignment()) - { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getSize().width); - av.setStartRes(vscroll.getValue() * rowSize); - av.setEndRes( (vscroll.getValue() + 1) * rowSize); - } - else - { - av.setStartSeq(offy); - av.setEndSeq(offy + - seqPanel.seqCanvas.getSize().height / av.getCharHeight()); - } - } - - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } - - if (av.getWrapAlignment() || !fastPaint) - { - repaint(); - } - else - { - idPanel.idCanvas.fastPaint(av.getStartSeq() - oldY); - seqPanel.seqCanvas.fastPaint(av.getStartRes() - oldX, - av.getStartSeq() - oldY); - - scalePanel.repaint(); - if (av.getShowAnnotation()) - { - annotationPanel.fastPaint(av.getStartRes() - oldX); - } - } - - } - - public void update(Graphics g) - { - paint(g); - } - - public void paint(Graphics g) - { - Dimension d = idPanel.idCanvas.getSize(); - idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); - annotationSpaceFillerHolder.setSize(d.width, - annotationPanel.getSize().height); - alabels.setSize(d.width, annotationPanel.getSize().height); - - alabels.repaint(); - idPanel.idCanvas.repaint(); - seqPanel.seqCanvas.repaint(); - scalePanel.repaint(); - annotationPanel.repaint(); - - if (av.getWrapAlignment()) - { - int max = av.alignment.getWidth() / - seqPanel.seqCanvas. - getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); - vscroll.setMaximum(max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); - } - else - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) + * Copyright (C) 2009 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 + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.appletgui; + +import java.awt.*; +import java.awt.event.*; + +import jalview.datamodel.*; + +public class AlignmentPanel extends Panel implements AdjustmentListener +{ + + public AlignViewport av; + + OverviewPanel overviewPanel; + + SeqPanel seqPanel; + + IdPanel idPanel; + + IdwidthAdjuster idwidthAdjuster; + + public AlignFrame alignFrame; + + ScalePanel scalePanel; + + AnnotationPanel annotationPanel; + + AnnotationLabels alabels; + + // this value is set false when selection area being dragged + boolean fastPaint = true; + + public AlignmentPanel(AlignFrame af, final AlignViewport av) + { + try + { + jbInit(); + } catch (Exception e) + { + e.printStackTrace(); + } + + alignFrame = af; + this.av = av; + seqPanel = new SeqPanel(av, this); + idPanel = new IdPanel(av, this); + 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); + annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); + scalePanelHolder.add(scalePanel, BorderLayout.CENTER); + seqPanelHolder.add(seqPanel, BorderLayout.CENTER); + + fontChanged(); + setScrollValues(0, 0); + + hscroll.addAdjustmentListener(this); + vscroll.addAdjustmentListener(this); + + addComponentListener(new ComponentAdapter() + { + public void componentResized(ComponentEvent evt) + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + repaint(); + } + }); + + Dimension d = calculateIdWidth(); + idPanel.idCanvas.setSize(d); + + hscrollFillerPanel.setSize(d.width, annotationPanel.getSize().height); + + 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 SequenceRenderer getSequenceRenderer() + { + return seqPanel.seqCanvas.sr; + } + + public FeatureRenderer getFeatureRenderer() + { + return seqPanel.seqCanvas.fr; + } + + 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())); + av.updateSequenceIdColours(); + 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); + + validate(); + repaint(); + + if (overviewPanel != null) + { + overviewPanel.updateOverviewImage(); + } + } + + public void setIdWidth(int w, int h) + { + idPanel.idCanvas.setSize(w, h); + idPanelHolder.setSize(w, idPanelHolder.getSize().height); + alabels.setSize(w, alabels.getSize().height); + validate(); + } + + Dimension calculateIdWidth() + { + if (av.nullFrame == null) + { + av.nullFrame = new Frame(); + av.nullFrame.addNotify(); + } + + Graphics g = av.nullFrame.getGraphics(); + + FontMetrics fm = g.getFontMetrics(av.font); + AlignmentI al = av.getAlignment(); + + int i = 0; + int idWidth = 0; + String id; + while (i < al.getHeight() && al.getSequenceAt(i) != null) + { + SequenceI s = al.getSequenceAt(i); + id = s.getDisplayId(av.getShowJVSuffix()); + + if (fm.stringWidth(id) > idWidth) + { + idWidth = fm.stringWidth(id); + } + i++; + } + + // Also check annotation label widths + i = 0; + if (al.getAlignmentAnnotation() != null) + { + fm = g.getFontMetrics(av.nullFrame.getFont()); + while (i < al.getAlignmentAnnotation().length) + { + String label = al.getAlignmentAnnotation()[i].label; + if (fm.stringWidth(label) > idWidth) + { + idWidth = fm.stringWidth(label); + } + i++; + } + } + + return new Dimension(idWidth, idPanel.idCanvas.getSize().height); + } + + public void highlightSearchResults(SearchResults results) + { + seqPanel.seqCanvas.highlightSearchResults(results); + } + /** + * scroll the view to show the position of the highlighted + * region in results (if any) + * @param results + */ + public void scrollToPosition(SearchResults results) + { + // do we need to scroll the panel? + if (results != null && results.getSize()>0) + { + int seqIndex = av.alignment.findIndex(results); + if (seqIndex==-1) + { + return; + } + SequenceI seq = av.alignment.getSequenceAt(seqIndex); + int [] r = results.getResults(seq, seq.getStart(), seq.getEnd()); + if (r==null) + { + return; + } + int start = r[0]; + int end = r[1]; + if (start<0) + { + return; + } + if (end==seq.getEnd()) + { + return; + } + 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 + { + 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() + { + return overviewPanel; + } + + public void setOverviewPanel(OverviewPanel op) + { + overviewPanel = op; + } + + public void setAnnotationVisible(boolean b) + { + if (!av.wrapAlignment) + { + annotationSpaceFillerHolder.setVisible(b); + annotationPanel.setVisible(b); + } + validate(); + repaint(); + } + + public void setWrapAlignment(boolean wrap) + { + av.startSeq = 0; + av.startRes = 0; + scalePanelHolder.setVisible(!wrap); + + hscroll.setVisible(!wrap); + idwidthAdjuster.setVisible(!wrap); + + if (wrap) + { + annotationPanel.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } + else if (av.showAnnotation) + { + 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; + + // return value is true if the scroll is valid + public boolean scrollUp(boolean up) + { + if (up) + { + if (vscroll.getValue() < 1) + { + return false; + } + setScrollValues(hscroll.getValue(), vscroll.getValue() - 1); + } + else + { + if (vextent + vscroll.getValue() >= av.getAlignment().getHeight()) + { + return false; + } + setScrollValues(hscroll.getValue(), vscroll.getValue() + 1); + } + + repaint(); + return true; + } + + public boolean scrollRight(boolean right) + { + if (!right) + { + if (hscroll.getValue() < 1) + { + return false; + } + setScrollValues(hscroll.getValue() - 1, vscroll.getValue()); + } + else + { + if (hextent + hscroll.getValue() >= av.getAlignment().getWidth()) + { + return false; + } + setScrollValues(hscroll.getValue() + 1, vscroll.getValue()); + } + + 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 + .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 > width) + { + hextent = width; + } + + if (vextent > height) + { + vextent = height; + } + + if ((hextent + x) > width) + { + x = width - hextent; + } + + if ((vextent + y) > height) + { + y = height - vextent; + } + + if (y < 0) + { + y = 0; + } + + if (x < 0) + { + x = 0; + } + + av.setStartSeq(y); + + int endSeq = y + vextent; + if (endSeq > av.alignment.getHeight()) + { + endSeq = av.alignment.getHeight(); + } + + av.setEndSeq(endSeq); + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + + if (overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + + } + + public void adjustmentValueChanged(AdjustmentEvent evt) + { + int oldX = av.getStartRes(); + int oldY = av.getStartSeq(); + + if (evt == null || evt.getSource() == hscroll) + { + int x = hscroll.getValue(); + av.setStartRes(x); + av.setEndRes(x + seqPanel.seqCanvas.getSize().width + / av.getCharWidth() - 1); + } + + if (evt == null || evt.getSource() == vscroll) + { + int offy = vscroll.getValue(); + if (av.getWrapAlignment()) + { + int rowSize = seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width); + av.setStartRes(vscroll.getValue() * rowSize); + av.setEndRes((vscroll.getValue() + 1) * rowSize); + } + else + { + av.setStartSeq(offy); + av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height + / av.getCharHeight()); + } + } + + if (overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + + int scrollX = av.startRes - oldX; + int scrollY = av.startSeq - oldY; + + if (av.getWrapAlignment() || !fastPaint || av.MAC) + { + repaint(); + } + else + { + // 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()) + { + annotationPanel.fastPaint(av.getStartRes() - oldX); + } + } + + } + + public void paintAlignment(boolean updateOverview) + { + repaint(); + + if (updateOverview) + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager().sequenceColoursChanged(this); + + if (overviewPanel != null) + { + overviewPanel.updateOverviewImage(); + } + } + } + + public void update(Graphics g) + { + paint(g); + } + + public void paint(Graphics g) + { + invalidate(); + Dimension d = idPanel.idCanvas.getSize(); + idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); + annotationSpaceFillerHolder.setSize(d.width, + annotationPanel.getSize().height); + + alabels.setSize(d.width, annotationPanel.getSize().height); + + if (av.getWrapAlignment()) + { + 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 + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + } + + alabels.repaint(); + + seqPanel.seqCanvas.repaint(); + scalePanel.repaint(); + annotationPanel.repaint(); + idPanel.idCanvas.repaint(); + } + + protected Panel sequenceHolderPanel = new Panel(); + + protected Scrollbar vscroll = new Scrollbar(); + + protected Scrollbar hscroll = new Scrollbar(); + + protected Panel seqPanelHolder = new Panel(); + + BorderLayout borderLayout1 = new BorderLayout(); + + BorderLayout borderLayout3 = new BorderLayout(); + + protected Panel scalePanelHolder = new Panel(); + + protected Panel idPanelHolder = new Panel(); + + BorderLayout borderLayout5 = new BorderLayout(); + + protected Panel idSpaceFillerPanel1 = new Panel(); + + public Panel annotationSpaceFillerHolder = new Panel(); + + BorderLayout borderLayout6 = new BorderLayout(); + + BorderLayout borderLayout7 = new BorderLayout(); + + Panel hscrollHolder = new Panel(); + + BorderLayout borderLayout10 = new BorderLayout(); + + protected Panel hscrollFillerPanel = new Panel(); + + BorderLayout borderLayout11 = new BorderLayout(); + + 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); + 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); + } + +}