X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=7f2a943d9425ee5a6958b35661f7d314d12844e1;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=7e42d34450dd2ddfd81dbff270db5343813a009c;hpb=7f93804f766c054832f87406d9c72c87cb5f3050;p=jalview.git diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java old mode 100755 new mode 100644 index 7e42d34..7f2a943 --- a/src/jalview/appletgui/AlignmentPanel.java +++ b/src/jalview/appletgui/AlignmentPanel.java @@ -1,29 +1,32 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.appletgui; import java.awt.*; import java.awt.event.*; +import jalview.api.AlignmentViewPanel; import jalview.datamodel.*; +import jalview.structure.StructureSelectionManager; -public class AlignmentPanel extends Panel implements AdjustmentListener +public class AlignmentPanel extends Panel implements AdjustmentListener, + AlignmentViewPanel { public AlignViewport av; @@ -47,6 +50,20 @@ public class AlignmentPanel extends Panel implements AdjustmentListener // 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 @@ -64,9 +81,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener scalePanel = new ScalePanel(av, this); idwidthAdjuster = new IdwidthAdjuster(this); annotationPanel = new AnnotationPanel(this); + annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER); - sequenceHolderPanel.add(annotationPanel, BorderLayout.SOUTH); - + sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH); alabels = new AnnotationLabels(this); setAnnotationVisible(av.showAnnotation); @@ -80,6 +97,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener fontChanged(); setScrollValues(0, 0); + apvscroll.addAdjustmentListener(this); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -88,8 +106,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public void componentResized(ComponentEvent evt) { setScrollValues(av.getStartRes(), av.getStartSeq()); + if (getSize().height > 0 + && annotationPanelHolder.getSize().height > 0) + { + validateAnnotationDimensions(false); + } repaint(); } + }); Dimension d = calculateIdWidth(); @@ -101,7 +125,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener annotationSpaceFillerHolder.setSize(d.width, annotationPanel.getSize().height); alabels.setSize(d.width, annotationPanel.getSize().height); - final AlignmentPanel ap = this; av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { @@ -114,7 +137,6 @@ public class AlignmentPanel extends Panel implements AdjustmentListener } } }); - } public SequenceRenderer getSequenceRenderer() @@ -153,14 +175,16 @@ public class AlignmentPanel extends Panel implements AdjustmentListener + fm.getDescent())); av.updateSequenceIdColours(); annotationPanel.image = null; - int ap = annotationPanel.adjustPanelHeight(); - annotationPanel.repaint(); + 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(); @@ -174,6 +198,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { idPanel.idCanvas.setSize(w, h); idPanelHolder.setSize(w, idPanelHolder.getSize().height); + annotationSpaceFillerHolder.setSize(w, + annotationSpaceFillerHolder.getSize().height); alabels.setSize(w, alabels.getSize().height); validate(); } @@ -225,73 +251,159 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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) + * 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 void scrollToPosition(SearchResults results) + 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) + if (results != null && results.getSize() > 0) { - int seqIndex = av.alignment.findIndex(results); - if (seqIndex==-1) + AlignmentI alignment = av.getAlignment(); + int seqIndex = alignment.findIndex(results); + if (seqIndex == -1) { - return; + return false; + } + SequenceI seq = alignment.getSequenceAt(seqIndex); + int[] r = results.getResults(seq, 0, 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; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); - int [] r = results.getResults(seq, seq.getStart(), seq.getEnd()); - if (r==null) + if (av.applet.debug) { - return; + // 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) + if (start < 0) { - return; + return false; } - if (end==seq.getEnd()) + if (end == seq.getEnd()) { - return; + return false; } - if (!av.wrapAlignment) + 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 ((av.getStartRes() > end) - || (av.getEndRes() < start) - || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart)) { - if (start > av.alignment.getWidth() - hextent) + // 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.getAlignment().getWidth() - hextent) + { + start = av.getAlignment().getWidth() - hextent; + if (start < 0) { - start = av.alignment.getWidth() - hextent; - if (start < 0) - { - start = 0; - } + start = 0; } - if (seqIndex > av.alignment.getHeight() - vextent) + + } + if (seqIndex > av.getAlignment().getHeight() - vextent) + { + seqIndex = av.getAlignment().getHeight() - vextent; + if (seqIndex < 0) { - seqIndex = av.alignment.getHeight() - vextent; - if (seqIndex < 0) - { - seqIndex = 0; - } + seqIndex = 0; } - setScrollValues(start, seqIndex); } - } - else - { - scrollToWrappedVisible(start); - } + // System.out.println("trying to scroll to: "+start+" "+seqIndex); + setScrollValues(start, seqIndex); + }/**/ } - - repaint(); + else + { + scrollToWrappedVisible(start); + } + if (redrawOverview && overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + paintAlignment(redrawOverview); + return true; } void scrollToWrappedVisible(int res) @@ -320,12 +432,99 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (!av.wrapAlignment) { annotationSpaceFillerHolder.setVisible(b); - annotationPanel.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 = av.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; + + if (adjustPanelHeight) + { + // NOTE: this logic is different in the application. Need a better algorithm to define behaviour + // sets initial preferred height + // try and set height according to alignment + float sscaling = (float) ((av.getCharHeight() * av.getAlignment().getHeight())/(1.0*mheight)); + if (sscaling > 0.5) + { + // if the alignment is too big then + // default is 0.5 split + height = seqandannot / 2; + } + else + { + // otherwise just set the panel so that one row of sequence is visible + height = -av.getCharHeight() * 1 + + (int) (seqandannot * (1 - sscaling)); + } + } + else + { + // 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; @@ -337,12 +536,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (wrap) { - annotationPanel.setVisible(false); + annotationPanelHolder.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } else if (av.showAnnotation) { - annotationPanel.setVisible(true); + annotationPanelHolder.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } @@ -408,17 +607,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener public void setScrollValues(int x, int y) { - int width = av.alignment.getWidth(); - int height = av.alignment.getHeight(); + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { width = av.getColumnSelection().findColumnPosition(width); } - - av.setStartRes(x); - av - .setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1); + if (x < 0) + { + x = 0; + } + ; hextent = seqPanel.seqCanvas.getSize().width / av.charWidth; vextent = seqPanel.seqCanvas.getSize().height / av.charHeight; @@ -435,6 +635,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if ((hextent + x) > width) { + System.err.println("hextent was " + hextent + " and x was " + x); + x = width - hextent; } @@ -450,18 +652,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (x < 0) { + System.err.println("x was " + x); x = 0; } av.setStartSeq(y); int endSeq = y + vextent; - if (endSeq > av.alignment.getHeight()) + if (endSeq > av.getAlignment().getHeight()) { - endSeq = av.alignment.getHeight(); + endSeq = av.getAlignment().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); @@ -469,6 +675,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener { overviewPanel.setBoxPosition(); } + sendViewPosition(); } @@ -477,6 +684,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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(); @@ -537,9 +753,17 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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(); @@ -547,7 +771,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (updateOverview) { jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + .getStructureSelectionManager(av.applet) + .sequenceColoursChanged(this); if (overviewPanel != null) { @@ -566,16 +791,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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(); + int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -586,7 +807,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener if (canvasWidth > 0) { int max = maxwidth / canvasWidth; - vscroll.setMaximum(max); + vscroll.setMaximum(1 + max); vscroll.setUnitIncrement(1); vscroll.setVisibleAmount(1); } @@ -642,6 +863,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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)); @@ -666,7 +893,13 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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); @@ -688,4 +921,46 @@ public class AlignmentPanel extends Panel implements AdjustmentListener 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) + { + updateAnnotation(applyGlobalSettings, false); + } + + public void updateAnnotation(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, + preserveNewGroupSettings); + adjustAnnotationHeight(); + } + + @Override + public AlignmentI getAlignment() + { + return av.getAlignment(); + } + + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return StructureSelectionManager + .getStructureSelectionManager(av.applet); + } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + // TODO: JAL-960 + System.err.println("Out of memory whilst '" + string + "'"); + error.printStackTrace(); + } + }