X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=ad7b9959a86a5794538273ad2aea3bc892272144;hb=cd05157564b53f68ca9eb3ade15d0e687b57572d;hp=0155a672df954c852bfa06d65360b29e31d6014f;hpb=299fbd01c9a02a8010cbba3885c1b958b15c16b2;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 0155a67..ad7b995 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle * * This file is part of Jalview. * @@ -20,7 +20,6 @@ package jalview.gui; import java.beans.*; import java.io.*; import java.util.Hashtable; -import java.util.Vector; import java.awt.*; import java.awt.event.*; @@ -32,7 +31,6 @@ import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; -import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; /** @@ -276,16 +274,16 @@ public class AlignmentPanel extends GAlignmentPanel implements // do we need to scroll the panel? // TODO: tons of nullpointereexceptions raised here. if (results != null && results.getSize() > 0 && av != null - && av.alignment != null) + && av.getAlignment() != null) { - int seqIndex = av.alignment.findIndex(results); + int seqIndex = av.getAlignment().findIndex(results); if (seqIndex == -1) { return false; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); - int[] r=results.getResults(seq, 0, av.alignment.getWidth()); + int[] r=results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; @@ -302,13 +300,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { return false; } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { start = av.getColumnSelection().findColumnPosition(start); end = av.getColumnSelection().findColumnPosition(end); if (start==end) { - if (!av.colSel.isVisible(r[0])) + if (!av.getColumnSelection().isVisible(r[0])) { // don't scroll - position isn't visible return false; @@ -547,14 +545,14 @@ public class AlignmentPanel extends GAlignmentPanel implements public void setScrollValues(int x, int y) { // System.err.println("Scroll to "+x+","+y); - if (av == null || av.alignment == null) + if (av == null || av.getAlignment() == null) { return; } - 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); } @@ -723,9 +721,9 @@ public class AlignmentPanel extends GAlignmentPanel implements 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; } @@ -849,7 +847,7 @@ public class AlignmentPanel extends GAlignmentPanel implements endSeq = av.getAlignment().getHeight(); } - int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight; + int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight; if (av.showAnnotation) { @@ -920,12 +918,16 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + if (av.showAnnotation && (endSeq == av.getAlignment().getHeight())) { + // draw annotation - need to offset for current scroll position + int offset=-alabels.scrollOffset; + pg.translate(0, offset); pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); alabels.drawComponent((Graphics2D) pg, idWidth); pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1); + annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1); + pg.translate(0, -offset); } return Printable.PAGE_EXISTS; @@ -971,8 +973,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int idWidth = getVisibleIdWidth(false); - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -998,10 +1000,10 @@ public class AlignmentPanel extends GAlignmentPanel implements do { - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { pg.setFont(idPanel.idCanvas.idfont); - SequenceI s = av.alignment.getSequenceAt(i); + SequenceI s = av.getAlignment().getSequenceAt(i); String string = s.getDisplayId(av.getShowJVSuffix()); int xPos = 0; if (av.rightAlignIds) @@ -1073,13 +1075,18 @@ public class AlignmentPanel extends GAlignmentPanel implements void makeAlignmentImage(int type, File file) { - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + long progress=System.currentTimeMillis(); + if (alignFrame!=null) { + alignFrame.setProgressBar("Saving "+(type == jalview.util.ImageMaker.PNG ? "PNG image":"EPS file") , progress); + } + try { + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - int height = ((av.alignment.getHeight() + 1) * av.charHeight) + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + scalePanel.getHeight(); int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); @@ -1111,19 +1118,17 @@ public class AlignmentPanel extends GAlignmentPanel implements { jalview.util.ImageMaker im; + final String imageAction,imageTitle; if (type == jalview.util.ImageMaker.PNG) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Create PNG image from alignment", width, height, file, - null); + imageAction="Create PNG image from alignment"; + imageTitle=null; + } else { + imageAction="Create EPS file from alignment"; + imageTitle=alignFrame.getTitle(); } - else - { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Create EPS file from alignment", width, height, file, - alignFrame.getTitle()); - } - + im = new jalview.util.ImageMaker(this, type, imageAction, width, height, file, + imageTitle); if (av.getWrapAlignment()) { if (im.getGraphics() != null) @@ -1151,6 +1156,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { ex.printStackTrace(); } + } + finally { + if (alignFrame!=null) + { + alignFrame.setProgressBar("Export complete.", progress); + } + } } /** @@ -1173,7 +1185,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS // //////////////////////////////////////////// - int idWidth = getVisibleIdWidth(true); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -1183,7 +1195,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment + int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment() .getWidth(), g, gSize, f, fSize, sy; StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); @@ -1196,15 +1208,15 @@ public class AlignmentPanel extends GAlignmentPanel implements { sy = s * av.charHeight + scaleHeight; - SequenceI seq = av.alignment.getSequenceAt(s); + SequenceI seq = av.getAlignment().getSequenceAt(s); SequenceFeature[] features = seq.getDatasetSequence() .getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + ""); @@ -1340,8 +1352,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -1365,7 +1377,7 @@ public class AlignmentPanel extends GAlignmentPanel implements jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); ssm.removeStructureViewerListener(seqPanel, null); ssm.removeSelectionListener(seqPanel); - av.alignment = null; + av.setAlignment(null); av = null; } else @@ -1382,79 +1394,22 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void updateAnnotation() { - updateAnnotation(false); + updateAnnotation(false, 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(); + updateAnnotation(applyGlobalSettings,false); + } + public void updateAnnotation(boolean applyGlobalSettings, boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, preserveNewGroupSettings); adjustAnnotationHeight(); } @Override public AlignmentI getAlignment() { - return av.alignment; + return av.getAlignment(); } /** @@ -1487,4 +1442,28 @@ public class AlignmentPanel extends GAlignmentPanel implements { return av.getStructureSelectionManager(); } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + new OOMWarning(string, error, this); + } + + public FeatureRenderer cloneFeatureRenderer() + { + + return new FeatureRenderer(this); + } + + public void updateFeatureRenderer(FeatureRenderer fr) + { + fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer()); + } + + public void updateFeatureRendererFrom(FeatureRenderer fr) + { + if (seqPanel.seqCanvas.getFeatureRenderer()!=null) { + seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr); + } + } }