X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=a1bc8732a64dad55ee57f70331d5d6e1a9dbfb25;hb=b61f2d9b571c4e4ab3285257c6ddbd39da61fa05;hp=f7f1b203b5f237c149edfcad4bb7dc4e677b2693;hpb=df9b85c1cf39894039018499fe802406cc37f209;p=jalview.git diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index f7f1b20..a1bc873 100755 --- a/src/jalview/appletgui/IdCanvas.java +++ b/src/jalview/appletgui/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 @@ -43,7 +43,7 @@ public class IdCanvas { setLayout(null); this.av = av; - PaintRefresher.Register(this, av.alignment); + PaintRefresher.Register(this, av.getSequenceSetId()); } public void drawIdString(Graphics gg, SequenceI s, int i, int starty, @@ -59,7 +59,7 @@ public class IdCanvas gg.setColor(Color.white); } else if (av.getSelectionGroup() != null && - av.getSelectionGroup().getSequences(false).contains(s)) + av.getSelectionGroup().getSequences(null).contains(s)) { gg.setColor(Color.lightGray); gg.fillRect(0, ((i - starty) * charHeight) + ypos, @@ -68,7 +68,7 @@ public class IdCanvas } else { - gg.setColor(s.getColor()); + gg.setColor(av.getSequenceColour(s)); gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width, charHeight); gg.setColor(Color.black); @@ -79,6 +79,9 @@ public class IdCanvas ((i - starty) * charHeight) + ypos + charHeight - (charHeight / 5)); + if (av.hasHiddenRows && av.showHiddenMarkers) + drawMarker(i, starty, ypos); + } public void fastPaint(int vertical) @@ -163,23 +166,32 @@ public class IdCanvas gg.setFont(italic); gg.fillRect(0, 0, getSize().width, getSize().height); - drawIds(av.getStartSeq(), av.endSeq); + drawIds(av.startSeq, av.endSeq); g.drawImage(image, 0, 0, this); } void drawIds(int starty, int endy) { + Font italic = new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()); + + gg.setFont(italic); + Color currentColor = Color.white; Color currentTextColor = Color.black; - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); 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; - if(av.showAnnotation) + if (av.showAnnotation) { AnnotationPanel ap = new AnnotationPanel(av); annotationHeight = ap.adjustPanelHeight(); @@ -190,82 +202,92 @@ public class IdCanvas 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 <= getSize().height) && (row < maxwidth); + ypos += cHeight, row += rowSize) + { + for (int i = starty; i < alheight; i++) + { + if (av.hasHiddenRows) + { + setHiddenFont(i); + } + else + gg.setFont(italic); + + SequenceI s = av.alignment.getSequenceAt(i); + drawIdString(gg, s, i, 0, ypos); + } - // Draw the rest of the panels - for (int ypos = hgap, row = av.startRes; - (ypos <= getSize().height) && (row < av.alignment.getWidth()); - ypos += cHeight, row += rowSize) + if (labels != null) { - for (int i = starty; i < av.alignment.getHeight(); i++) - { - SequenceI s = av.alignment.getSequenceAt(i); - gg.setFont(italic); - drawIdString(gg, s, i, 0, ypos); - } - - if(labels!=null) - { - gg.translate(0, ypos+(av.getAlignment().getHeight() * av.charHeight)); - labels.drawComponent(gg, getSize().width); - gg.translate(0, -ypos-(av.getAlignment().getHeight() * av.charHeight)); - } + gg.translate(0, ypos + (alheight * av.charHeight)); + labels.drawComponent(gg, getSize().width); + gg.translate(0, -ypos - (alheight * av.charHeight)); } + } } else { + //Now draw the id strings //Now draw the id strings + SequenceI seq; for (int i = starty; i < endy; i++) { - // Selected sequence colours + if (av.hasHiddenRows) + { + setHiddenFont(i); + } - if (searchResults != null && - searchResults.contains(av.alignment.getSequenceAt(i))) + seq = av.alignment.getSequenceAt(i); + if(seq==null) + continue; + + // Selected sequence colours + if ( (searchResults != null) && + searchResults.contains(seq)) { - gg.setColor(Color.black); currentColor = Color.black; currentTextColor = Color.white; } - else if (av.getSelectionGroup() != null - && - av.getSelectionGroup().getSequences(false).contains(av.alignment. - getSequenceAt(i))) + else if ( (av.getSelectionGroup() != null) && + av.getSelectionGroup().getSequences(null).contains(seq)) { currentColor = Color.lightGray; currentTextColor = Color.black; } else { - currentColor = av.alignment.getSequenceAt(i).getColor(); + currentColor = av.getSequenceColour(seq); currentTextColor = Color.black; } gg.setColor(currentColor); - gg.fillRect(0, - ((i - starty) * av.charHeight), - getSize().width, + gg.fillRect(0, (i - starty) * av.charHeight, getSize().width, av.charHeight); gg.setColor(currentTextColor); - gg.drawString(av.alignment.getSequenceAt(i) - .getDisplayId(av.getShowJVSuffix()), 0, - ((i - starty) * av.charHeight) + - av.charHeight - (av.charHeight / 5)); - } - // add a border - gg.setColor(Color.white); - gg.fillRect(getSize().width - 4, 0, 4, getSize().height); - } + gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), + 0, + ( ( (i - starty) * av.charHeight) + av.charHeight) - + (av.charHeight / 5)); + if (av.hasHiddenRows && av.showHiddenMarkers) + drawMarker(i, starty, 0); + } + } } public void setHighlighted(java.util.Vector found) @@ -273,4 +295,74 @@ public class IdCanvas searchResults = found; repaint(); } + + 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; + + boolean below = (hiddenIndex > lastIndex + 1); + boolean above = (nextIndex > hiddenIndex + 1); + + + + for(int j=0; j