X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=71cc48344d6380a0038dc8e8337b0aaee04245dd;hb=3e6b14950a06bb87c147493e4dfff0c4491ea25b;hp=2951c14358db46c7710dd01ca1981bcb2c7b1ce9;hpb=ce728f87f1f43be3041ef02f7f2cc2e39314711a;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 2951c14..71cc483 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -18,8 +18,6 @@ */ package jalview.gui; -import jalview.analysis.*; - import jalview.datamodel.*; import java.awt.*; @@ -45,6 +43,10 @@ public class IdCanvas extends JPanel int imgHeight = 0; boolean fastPaint = false; java.util.Vector searchResults; + FontMetrics fm; + AnnotationLabels labels = null; + AnnotationPanel ap; + Font idfont; /** * Creates a new IdCanvas object. @@ -55,7 +57,7 @@ public class IdCanvas extends JPanel { setLayout(new BorderLayout()); this.av = av; - PaintRefresher.Register(this, av.alignment); + PaintRefresher.Register(this, av.getSequenceSetId()); } /** @@ -67,9 +69,10 @@ public class IdCanvas extends JPanel * @param starty DOCUMENT ME! * @param ypos DOCUMENT ME! */ - public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, - int ypos) + public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos) { + int xPos = 0; + int panelWidth = getWidth(); int charHeight = av.charHeight; if ((searchResults != null) && searchResults.contains(s)) @@ -80,7 +83,7 @@ public class IdCanvas extends JPanel gg.setColor(Color.white); } else if ((av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains(s)) + av.getSelectionGroup().getSequences(null).contains(s)) { gg.setColor(Color.lightGray); gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), @@ -89,21 +92,26 @@ public class IdCanvas extends JPanel } else { - gg.setColor(s.getColor()); + gg.setColor(av.getSequenceColour(s)); gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); gg.setColor(Color.black); } - String string = s.getName(); - - if (av.getShowFullId()) + if (av.rightAlignIds) { - string = s.getDisplayId(); + xPos = panelWidth - fm.stringWidth( + s.getDisplayId(av.getShowJVSuffix()) + ) - 4; } - gg.drawString(string, 0, - (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); + gg.drawString( s.getDisplayId(av.getShowJVSuffix()), + xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); + + if (av.hasHiddenRows && av.showHiddenMarkers) + drawMarker(i, starty, ypos); + + } /** @@ -177,6 +185,8 @@ public class IdCanvas extends JPanel return; } + int oldHeight = imgHeight; + imgHeight = getHeight(); imgHeight -= (imgHeight % av.charHeight); @@ -185,19 +195,17 @@ public class IdCanvas extends JPanel return; } - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); + if(oldHeight!=imgHeight || image.getWidth(this)!=getWidth()) + { + image = new BufferedImage(getWidth(), imgHeight, + BufferedImage.TYPE_INT_RGB); + } + gg = (Graphics2D) image.getGraphics(); //Fill in the background gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); - gg.setFont(italic); drawIds(av.getStartSeq(), av.endSeq); @@ -212,92 +220,222 @@ public class IdCanvas extends JPanel */ void drawIds(int starty, int endy) { + if(av.seqNameItalics) + idfont = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + else + idfont = av.getFont(); + + gg.setFont(idfont); + fm = gg.getFontMetrics(); + + if (av.antiAlias) + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + Color currentColor = Color.white; Color currentTextColor = Color.black; if (av.getWrapAlignment()) { + int maxwidth = av.alignment.getWidth(); + int alheight = av.alignment.getHeight(); + + if (av.hasHiddenColumns) + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + int annotationHeight = 0; + if(av.showAnnotation) { - AnnotationPanel ap = new AnnotationPanel(av); + if (ap == null) + ap = new AnnotationPanel(av); + annotationHeight = ap.adjustPanelHeight(); + if (labels == null) + labels = new AnnotationLabels(av); } int hgap = av.charHeight; if (av.scaleAboveWrapped) hgap += av.charHeight; - int cHeight = av.getAlignment().getHeight() * av.charHeight + int cHeight = alheight * av.charHeight + hgap + annotationHeight; - int rowSize = av.getEndRes() - av.getStartRes(); + int rowSize = av.getEndRes() - av.getStartRes(); + // Draw the rest of the panels for (int ypos = hgap, row = av.startRes; - (ypos <= getHeight()) && (row < av.alignment.getWidth()); + (ypos <= getHeight()) && (row < maxwidth); ypos += cHeight, row += rowSize) { - for (int i = starty; i < av.alignment.getHeight(); i++) + for (int i = starty; i < alheight; i++) + { + SequenceI s = av.alignment.getSequenceAt(i); + if (av.hasHiddenRows) + { + setHiddenFont(s); + } + else + gg.setFont(idfont); + + drawIdString(gg, s, i, 0, ypos); + } + + if(labels!=null && av.showAnnotation) { - SequenceI s = av.alignment.getSequenceAt(i); - drawIdString(gg, s, i, 0, ypos); + gg.translate(0, ypos+(alheight * av.charHeight)); + labels.drawComponent(gg, getWidth()); + gg.translate(0, -ypos-(alheight * av.charHeight)); } } } else { + //No need to hang on to labels if we're not wrapped + labels = null; + + //Now draw the id strings + int panelWidth = getWidth(); + int xPos = 0; + + SequenceI sequence; //Now draw the id strings for (int i = starty; i < endy; i++) { + sequence = av.alignment.getSequenceAt(i); + + if(sequence==null) + continue; + + if (av.hasHiddenRows) + { + setHiddenFont(sequence); + } + // Selected sequence colours - if ((searchResults != null) && - searchResults.contains(av.alignment.getSequenceAt(i))) + if ( (searchResults != null) && + searchResults.contains(sequence)) { - gg.setColor(Color.black); - currentColor = Color.black; - currentTextColor = Color.white; + currentColor = Color.black; + currentTextColor = Color.white; } - else if ((av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains( - av.alignment.getSequenceAt(i))) + else if ( (av.getSelectionGroup() != null) && + av.getSelectionGroup().getSequences(null).contains( + sequence)) { - currentColor = Color.lightGray; - currentTextColor = Color.black; + currentColor = Color.lightGray; + currentTextColor = Color.black; } else { - currentColor = av.alignment.getSequenceAt(i).getColor(); - currentTextColor = Color.black; + currentColor = av.getSequenceColour(sequence); + currentTextColor = Color.black; } gg.setColor(currentColor); gg.fillRect(0, (i - starty) * av.charHeight, getWidth(), - av.charHeight); + av.charHeight); gg.setColor(currentTextColor); - String string = av.alignment.getSequenceAt(i).getName(); + String string = sequence.getDisplayId( av.getShowJVSuffix()); - if (av.getShowFullId()) + + if(av.rightAlignIds) { - string = av.alignment.getSequenceAt(i).getDisplayId(); + xPos = panelWidth - fm.stringWidth(string) - 4; } - gg.drawString(string, 0, + gg.drawString(string, xPos, (((i - starty) * av.charHeight) + av.charHeight) - (av.charHeight / 5)); + + if(av.hasHiddenRows && av.showHiddenMarkers) + drawMarker(i, starty, 0); + } - // add a border - gg.setColor(Color.white); - gg.fillRect(getWidth() - 4, 0, 4, getHeight()); } } + void drawMarker(int i, int starty, int yoffset) + { + + SequenceI [] hseqs = av.alignment.getHiddenSequences().hiddenSequences; + //Use this method here instead of calling hiddenSeq adjust + //3 times. + int hSize = hseqs.length; + + int hiddenIndex = i; + int lastIndex = i - 1; + int nextIndex = i + 1; + + for(int j=0; j lastIndex + 1); + boolean above = (nextIndex > hiddenIndex+1); + + + gg.setColor(Color.blue); + if(below) + { + gg.fillPolygon(new int[] + {getWidth()- av.charHeight, + getWidth()- av.charHeight, + getWidth()}, + new int[] + { + (i - starty) * av.charHeight +yoffset, + (i - starty) * av.charHeight +yoffset+ av.charHeight / 4, + (i - starty) * av.charHeight+yoffset + }, 3); + } + if(above) + { + gg.fillPolygon(new int[] + {getWidth()- av.charHeight, + getWidth()- av.charHeight, + getWidth() }, + new int[] + { + (i - starty+1) * av.charHeight +yoffset, + (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4, + (i - starty+1) * av.charHeight +yoffset + }, 3); + + } + } + + void setHiddenFont(SequenceI seq) + { + Font bold = new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); + + + if (av.hiddenRepSequences!=null && + av.hiddenRepSequences.containsKey(seq)) + gg.setFont(bold); + else + gg.setFont(idfont); + } + /** * DOCUMENT ME! *