X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=efefeafbada38512aa86f69d4377d8d6675873eb;hb=cf25e4f4f7d2cb2a7847a01d7cbe52003b46bf54;hp=608d29f20eb1b818fa5974aba25925e804a51f0e;hpb=0bc7bf031e9a20267bdc1e38fea24ebb64f4cca4;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 608d29f..efefeaf 100755 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,25 +1,26 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 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. * - * 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 + * 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 Jalview. If not, see . */ package jalview.gui; import java.beans.*; import java.io.*; +import java.util.Hashtable; +import java.util.Vector; import java.awt.*; import java.awt.event.*; @@ -71,9 +72,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * Creates a new AlignmentPanel object. * * @param af - * DOCUMENT ME! + * DOCUMENT ME! * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -178,8 +179,8 @@ public class AlignmentPanel extends GAlignmentPanel implements AlignmentI al = av.getAlignment(); int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth - / 3)); + int maxwidth = Math.max(20, + Math.min(afwidth - 200, (int) 2 * afwidth / 3)); int i = 0; int idWidth = 0; String id; @@ -225,76 +226,101 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param results - * DOCUMENT ME! + * DOCUMENT ME! */ 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 + * scroll the view to show the position of the highlighted region in results + * (if any) and redraw the overview + * * @param results */ - public boolean 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) + * 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) + * @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) { - // TODO: properly locate search results in view when large numbers of hidden columns exist before highlighted region + public boolean scrollToPosition(SearchResults results, + boolean redrawOverview) + { + int startv, endv, starts, ends, width; + // TODO: properly locate search results in view when large numbers of hidden + // columns exist before highlighted region // do we need to scroll the panel? // TODO: tons of nullpointereexceptions raised here. - if (results != null && results.getSize()>0 && av!=null && av.alignment!=null) + if (results != null && results.getSize() > 0 && av != null + && av.alignment != null) { int seqIndex = av.alignment.findIndex(results); - if (seqIndex==-1) + if (seqIndex == -1) { return false; } SequenceI seq = av.alignment.getSequenceAt(seqIndex); - - int [] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq, seq.getStart(), seq.getEnd()); - if (r==null) + + int[] r = results.getResults(seq, 0, av.alignment.getWidth()); // results.getResults(seq, + // seq.getStart(), + // seq.getEnd()); + // TODO: VAMSAS: fix hidden column issue where scroll to left from C + // terminus is not visible + if (r == null) { return false; } int start = r[0]; int end = r[1]; - if (start<0) + // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // + // DEBUG + if (start < 0) { return false; } - if (end==seq.getEnd()) + if (end == seq.getEnd()) { return false; } if (!av.wrapAlignment) { - if ((av.getStartRes() >= start) - || (av.getEndRes() <= end)) + if ((startv = av.getStartRes()) >= start) + { + setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) { - setScrollValues(start-1, seqIndex); - } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)) + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), seqIndex); } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } } else { scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel!=null) + if (!redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); - } + } paintAlignment(!redrawOverview); return true; } @@ -303,7 +329,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int cwidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth)) + if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); av.startRes = vscroll.getValue() * cwidth; @@ -325,7 +351,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param op - * DOCUMENT ME! + * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { @@ -336,7 +362,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * DOCUMENT ME! */ public void setAnnotationVisible(boolean b) { @@ -376,6 +402,7 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); + addNotify(); repaint(); } @@ -383,7 +410,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param wrap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean wrap) { @@ -441,7 +468,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param right - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -477,13 +504,14 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param x - * DOCUMENT ME! + * DOCUMENT ME! * @param y - * DOCUMENT ME! + * DOCUMENT ME! */ public void setScrollValues(int x, int y) { - if (av==null || av.alignment==null) + // System.err.println("Scroll to "+x+","+y); + if (av == null || av.alignment == null) { return; } @@ -538,7 +566,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -550,9 +578,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int x = hscroll.getValue(); av.setStartRes(x); - av - .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av - .getCharWidth())) - 1); + av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -649,7 +675,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -692,16 +718,16 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pf - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException @@ -725,18 +751,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -832,8 +858,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av - .getCharHeight()); + pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, + av.getCharHeight()); pg.setColor(currentTextColor); @@ -846,7 +872,9 @@ public class AlignmentPanel extends GAlignmentPanel implements - 4; } - pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, + pg.drawString( + seq.getDisplayId(av.getShowJVSuffix()), + xPos, (((i - startSeq) * av.charHeight) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -872,18 +900,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -1264,25 +1292,103 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * close the panel - deregisters all listeners and nulls any references to alignment data. + * close the panel - deregisters all listeners and nulls any references to + * alignment data. */ public void closePanel() { - jalview.structure.StructureSelectionManager ssm = - jalview.structure.StructureSelectionManager + jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager .getStructureSelectionManager(); ssm.removeStructureViewerListener(seqPanel, null); ssm.removeSelectionListener(seqPanel); PaintRefresher.RemoveComponent(seqPanel.seqCanvas); PaintRefresher.RemoveComponent(idPanel.idCanvas); PaintRefresher.RemoveComponent(this); - if (av!=null) { + if (av != null) + { av.alignment = null; av = null; - } else { - if (Cache.log.isDebugEnabled()) { + } + else + { + if (Cache.log.isDebugEnabled()) + { Cache.log.warn("Closing alignment panel which is already closed."); } } } + + /** + * 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(); + } }