X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=224b9662359b356a1439eab748683eede64c58e5;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=0423cbb37abbeb5852dd662d5a21882cea886ffb;hpb=df1c58f9669c477db082016aa919d6c6cc9da071;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java old mode 100755 new mode 100644 index 0423cbb..224b966 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,567 +1,983 @@ -/* - * 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.datamodel.*; - -public class AlignmentPanel extends Panel 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; - - boolean MAC = false; - - public AlignmentPanel(AlignFrame af, final AlignViewport av) - { - try - { - jbInit(); - } - catch (Exception e) - { - e.printStackTrace(); - } - - if(System.getProperty("os.name").startsWith("Mac")) - MAC = true; - - 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); - - 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); - - 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); - 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); - - } - - - 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())); - - 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() - { - 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); - 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(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(SearchResults results) - { - seqPanel.seqCanvas.highlightSearchResults(results); - - // do we need to scroll the panel? - if (results != null) - { - 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 - { - int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getSize().width); - if (start < av.getStartRes() || start > (av.getStartRes() + cwidth)) - { - vscroll.setValue(start / cwidth); - av.startRes = vscroll.getValue() * cwidth; - } - } - } - - repaint(); - } - - public OverviewPanel getOverviewPanel() - { - return overviewPanel; - } - - public void setOverviewPanel(OverviewPanel op) - { - overviewPanel = op; - } - - public void setAnnotationVisible(boolean b) - { - if (!av.wrapAlignment) - { - annotationSpaceFillerHolder.setVisible(b); - annotationScroller.setVisible(b); - } - validate(); - repaint(); - } - - public void setWrapAlignment(boolean wrap) - { - av.startSeq = 0; - scalePanelHolder.setVisible(!wrap); - - - hscroll.setVisible(!wrap); - idwidthAdjuster.setVisible(!wrap); - - if (wrap) - { - annotationScroller.setVisible(false); - annotationSpaceFillerHolder.setVisible(false); - } - else if (av.showAnnotation) - { - annotationScroller.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; - } - 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==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 || MAC) - { - repaint(); - } - else if(!seqPanel.seqCanvas.fastPaint) - { - // 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. + */ +package jalview.appletgui; + +import java.awt.*; +import java.awt.event.*; +import java.util.Hashtable; +import java.util.Vector; + +import jalview.api.AlignmentViewPanel; +import jalview.datamodel.*; +import jalview.structure.StructureSelectionManager; + +public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel +{ + + 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 void finalize() { + alignFrame=null; + av=null; + seqPanel=null; + seqPanelHolder=null; + sequenceHolderPanel=null; + scalePanel=null; + scalePanelHolder=null; + annotationPanel=null; + annotationPanelHolder=null; + annotationSpaceFillerHolder=null; + } + 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); + annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER); + + sequenceHolderPanel.add(annotationPanelHolder, 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); + + apvscroll.addAdjustmentListener(this); + hscroll.addAdjustmentListener(this); + vscroll.addAdjustmentListener(this); + + addComponentListener(new ComponentAdapter() + { + public void componentResized(ComponentEvent evt) + { + setScrollValues(av.getStartRes(), av.getStartSeq()); + if (getSize().height>0 && annotationPanelHolder.getSize().height>0) { + validateAnnotationDimensions(false); + } + 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(false); + 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); + + validateAnnotationDimensions(false); + annotationPanel.repaint(); + 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); + annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.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); + } + + /** + * Highlight the given results on the alignment. + * + */ + public void highlightSearchResults(SearchResults results) + { + scrollToPosition(results); + seqPanel.seqCanvas.highlightSearchResults(results); + } + + /** + * scroll the view to show the position of the highlighted region in results + * (if any) and redraw the overview + * + * @param results + * @return false if results were not found + */ + public boolean scrollToPosition(SearchResults results) + { + return scrollToPosition(results, true); + } + + /** + * scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param results + * @param redrawOverview + * - when set, the overview will be recalculated (takes longer) + * @return false if results were not found + */ + public boolean scrollToPosition(SearchResults results, + boolean redrawOverview) + { + + // do we need to scroll the panel? + if (results != null && results.getSize() > 0) + { + int seqIndex = av.alignment.findIndex(results); + if (seqIndex == -1) + { + return false; + } + SequenceI seq = av.alignment.getSequenceAt(seqIndex); + int[] r = results.getResults(seq, 0,av.alignment.getWidth()); + if (r == null) + { + if (av.applet.debug) {// DEBUG + System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd()); + } + return false; + } + if (av.applet.debug) { + // DEBUG + /*System.out.println("DEBUG: scroll: start=" + r[0] + + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] + + " seq.end=" + seq.getEnd() + " av.getEndRes()=" + + av.getEndRes() + " hextent=" + hextent); + */ + } + int start = r[0]; + int end = r[1]; + if (start < 0) + { + return false; + } + if (end == seq.getEnd()) + { + return false; + } + return scrollTo(start, end, seqIndex, false, redrawOverview); + } + return true; + } + public boolean scrollTo(int ostart, int end, int seqIndex, boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends, width; + + int start=-1; + if (av.hasHiddenColumns) + { + start = av.getColumnSelection().findColumnPosition(ostart); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) + { + if (!scrollToNearest && !av.colSel.isVisible(ostart)) + { + // don't scroll - position isn't visible + return false; + } + } + } + else + { + start = ostart; + } + if (!av.wrapAlignment) + { + /* + int spos=av.getStartRes(),sqpos=av.getStartSeq(); + if ((startv = av.getStartRes()) >= start) + { + spos=start-1; +// seqIn +// setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { +// setScrollValues(spos=startv + 1 + end - endv, seqIndex); + spos=startv + 1 + end - endv; + } + else if ((starts = av.getStartSeq()) > seqIndex) + { + setScrollValues(av.getStartRes(), seqIndex); + } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } + + /* */ + 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; + } + } + // System.out.println("trying to scroll to: "+start+" "+seqIndex); + setScrollValues(start, seqIndex); + }/**/ + } + else + { + scrollToWrappedVisible(start); + } + if (redrawOverview && overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + paintAlignment(redrawOverview); + return true; + } + + 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); + annotationPanelHolder.setVisible(b); + } + validate(); + repaint(); + } + + /** + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. + */ + public void adjustAnnotationHeight() + { + // TODO: display vertical annotation scrollbar if necessary + // this is called after loading new annotation onto alignment + if (alignFrame.getSize().height == 0) + { + System.out.println("NEEDS FIXING"); + } + fontChanged(); + validateAnnotationDimensions(true); + apvscroll.addNotify(); + hscroll.addNotify(); + validate(); + paintAlignment(true); + } + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) { + boolean modified=false; + int height = annotationPanel.calcPanelHeight(); + int minsize=0; + if (hscroll.isVisible()) + { + height += (minsize=hscroll.getPreferredSize().height); + } + if (apvscroll.isVisible()) { + minsize+=apvscroll.getPreferredSize().height; + } + int mheight = height; + Dimension d=sequenceHolderPanel.getSize(),e=idPanel.getSize(); + int seqandannot=d.height-scalePanelHolder.getSize().height; + // sets initial preferred height + if ((height+40) > seqandannot / 2) + { + height = seqandannot / 2; + } + if (!adjustPanelHeight) + { + // maintain same window layout whilst updating sliders + height=annotationPanelHolder.getSize().height; + } + + if (seqandannot-height<5) + { + height = seqandannot; + } + annotationPanel.setSize(new Dimension(d.width,height)); + alabels.setSize(new Dimension(e.width,height)); + annotationSpaceFillerHolder.setSize(new Dimension(e.width, height)); + annotationPanelHolder.setSize(new Dimension(d.width, height)); + seqPanelHolder.setSize(d.width,seqandannot-height); + seqPanel.seqCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height); + int s=apvscroll.getValue(); + if (s>mheight-height) + { + s = 0; + } + apvscroll.setValues(s, height, 0, mheight); + annotationPanel.setScrollOffset(apvscroll.getValue()); + alabels.setScrollOffset(apvscroll.getValue()); + } + + public void setWrapAlignment(boolean wrap) + { + av.startSeq = 0; + av.startRes = 0; + scalePanelHolder.setVisible(!wrap); + + hscroll.setVisible(!wrap); + idwidthAdjuster.setVisible(!wrap); + + if (wrap) + { + annotationPanelHolder.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } + else if (av.showAnnotation) + { + annotationPanelHolder.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); + } + if (x<0) { x = 0; }; + + 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) + { + System.err.println("hextent was "+hextent+" and x was "+x); + + x = width - hextent; + } + + if ((vextent + y) > height) + { + y = height - vextent; + } + + if (y < 0) + { + y = 0; + } + + if (x < 0) + { + System.err.println("x was "+x); + x = 0; + } + + av.setStartSeq(y); + + int endSeq = y + vextent; + if (endSeq > av.alignment.getHeight()) + { + endSeq = av.alignment.getHeight(); + } + + av.setEndSeq(endSeq); + av.setStartRes(x); + av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + + if (overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + sendViewPosition(); + + + } + + public void adjustmentValueChanged(AdjustmentEvent evt) + { + int oldX = av.getStartRes(); + int oldY = av.getStartSeq(); + + if (evt == null || evt.getSource() == apvscroll) + { + annotationPanel.setScrollOffset(apvscroll.getValue()); + alabels.setScrollOffset(apvscroll.getValue()); + // annotationPanel.image=null; + // alabels.image=null; + // alabels.repaint(); + // annotationPanel.repaint(); + } + 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); + } + } + sendViewPosition(); + + } + private void sendViewPosition() + { + StructureSelectionManager.getStructureSelectionManager(av.applet).sendViewPosition(this, av.startRes, av.endRes, av.startSeq, av.endSeq); + } + + public void paintAlignment(boolean updateOverview) + { + repaint(); + + if (updateOverview) + { + jalview.structure.StructureSelectionManager + .getStructureSelectionManager(av.applet).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); + + 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(1 + 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(); + + Panel annotationPanelHolder = new Panel(); + + protected Scrollbar apvscroll = new Scrollbar(); + + BorderLayout borderLayout12 = 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); + apvscroll.setOrientation(Scrollbar.VERTICAL); + apvscroll.setVisible(true); + apvscroll.addAdjustmentListener(this); + + annotationPanelHolder.setBackground(Color.white); + annotationPanelHolder.setLayout(borderLayout12); + annotationPanelHolder.add(apvscroll, BorderLayout.EAST); + // 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); + } + + /** + * hides or shows dynamic annotation rows based on groups and av state flags + */ + public void updateAnnotation() + { + updateAnnotation(false); + } + + public void updateAnnotation(boolean applyGlobalSettings) + { + // TODO: this should be merged with other annotation update stuff - that + // sits on AlignViewport + boolean updateCalcs = false; + boolean conv = av.isShowGroupConservation(); + boolean cons = av.isShowGroupConsensus(); + boolean showprf = av.isShowSequenceLogo(); + boolean showConsHist = av.isShowConsensusHistogram(); + + boolean sortg = true; + + // remove old automatic annotation + // add any new annotation + + Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); + // intersect alignment annotation with alignment groups + + AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); + Hashtable oldrfs = new Hashtable(); + if (aan != null) + { + for (int an = 0; an < aan.length; an++) + { + if (aan[an].autoCalculated && aan[an].groupRef != null) + { + oldrfs.put(aan[an].groupRef, aan[an].groupRef); + av.alignment.deleteAnnotation(aan[an]); + aan[an] = null; + } + } + } + SequenceGroup sg; + if (gr != null) + { + for (int g = 0; g < gr.size(); g++) + { + updateCalcs = false; + sg = (SequenceGroup) gr.elementAt(g); + if (applyGlobalSettings || !oldrfs.containsKey(sg)) + { + // set defaults for this group's conservation/consensus + sg.setshowSequenceLogo(showprf); + sg.setShowConsensusHistogram(showConsHist); + } + if (conv) + { + updateCalcs = true; + av.alignment.addAnnotation(sg.getConservationRow(), 0); + } + if (cons) + { + updateCalcs = true; + av.alignment.addAnnotation(sg.getConsensus(), 0); + } + // refresh the annotation rows + if (updateCalcs) + { + sg.recalcConservation(); + } + } + } + oldrfs.clear(); + adjustAnnotationHeight(); + } + + @Override + public AlignmentI getAlignment() + { + return av.alignment; + } + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager.getStructureSelectionManager(av.applet); + } + +}