X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=c9ed3051c6790c454183b10d6faf8fd5db4dfeb3;hb=b149069ca631eb2e2c56c900ff4f490af1e98972;hp=9b1f10df0e5ae6a4899eb92849a2ea74f185abf5;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 9b1f10d..c9ed305 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 @@ -53,7 +53,7 @@ public class IdCanvas extends JPanel { setLayout(new BorderLayout()); this.av = av; - PaintRefresher.Register(this, av.alignment); + PaintRefresher.Register(this, av.getSequenceSetId()); } /** @@ -65,8 +65,7 @@ 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 charHeight = av.charHeight; @@ -78,7 +77,7 @@ public class IdCanvas extends JPanel gg.setColor(Color.white); } else if ((av.getSelectionGroup() != null) && - av.getSelectionGroup().sequences.contains(s)) + av.getSelectionGroup().getSequences(false).contains(s)) { gg.setColor(Color.lightGray); gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), @@ -87,21 +86,20 @@ 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()) - { - string = s.getDisplayId(); - } + gg.drawString( s.getDisplayId(av.getShowJVSuffix()), + 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); + + if (av.hasHiddenRows && av.showHiddenMarkers) + drawMarker(i, starty, ypos); + - gg.drawString(string, 0, - (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); } /** @@ -175,6 +173,8 @@ public class IdCanvas extends JPanel return; } + int oldHeight = imgHeight; + imgHeight = getHeight(); imgHeight -= (imgHeight % av.charHeight); @@ -183,15 +183,17 @@ public class IdCanvas extends JPanel return; } - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) image.getGraphics(); + 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); - drawIds(av.getStartSeq(), av.endSeq); g.drawImage(image, 0, 0, this); @@ -207,15 +209,24 @@ public class IdCanvas extends JPanel { Font italic = new Font(av.getFont().getName(), Font.ITALIC, av.getFont().getSize()); + gg.setFont(italic); - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + + 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; AnnotationLabels labels = null; @@ -230,84 +241,174 @@ public class IdCanvas extends JPanel 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++) + { + if (av.hasHiddenRows) { - SequenceI s = av.alignment.getSequenceAt(i); - drawIdString(gg, s, i, 0, ypos); + setHiddenFont(i); } + else + gg.setFont(italic); + + SequenceI s = av.alignment.getSequenceAt(i); + drawIdString(gg, s, i, 0, ypos); + } if(labels!=null) { - gg.setFont(av.getFont()); - gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight)); + gg.translate(0, ypos+(alheight * av.charHeight)); labels.drawComponent(gg, getWidth()); - gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight)); - gg.setFont(italic); + gg.translate(0, -ypos-(alheight * av.charHeight)); } + + } } else { + //Now draw the id strings + + 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(i); + } + // 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(false).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(); - - if (av.getShowFullId()) - { - string = av.alignment.getSequenceAt(i).getDisplayId(); - } + String string = sequence.getDisplayId( av.getShowJVSuffix()); gg.drawString(string, 0, (((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(int i) + { + Font italic = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + Font bold = new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); + + + if (av.alignment.getSequenceAt(i)!=null + && av.alignment.getSequenceAt(i).getHiddenSequences() != null) + gg.setFont(bold); + else + gg.setFont(italic); + } + /** * DOCUMENT ME! *