X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=ac82e12a36e8925fd8478c825e4e2bfc3c05cf6d;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=013c7a1a22858def959b11ef606ddb5d5a316d30;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java index 013c7a1..ac82e12 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 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, @@ -54,33 +54,34 @@ public class IdCanvas if (searchResults != null && searchResults.contains(s)) { gg.setColor(Color.black); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, + gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getSize().width, charHeight); 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, + gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getSize().width, charHeight); gg.setColor(Color.white); } else { - gg.setColor(s.getColor()); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, + gg.setColor(av.getSequenceColour(s)); + gg.fillRect(0, ( (i - starty) * charHeight) + ypos, getSize().width, charHeight); gg.setColor(Color.black); } - - gg.drawString( s.getDisplayId(av.getShowJVSuffix()), 0, - ((i - starty) * charHeight) + ypos + + gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0, + ( (i - starty) * charHeight) + ypos + charHeight - (charHeight / 5)); if (av.hasHiddenRows && av.showHiddenMarkers) - drawMarker(i, starty, ypos); + { + drawMarker(i, starty, ypos); + } } @@ -186,7 +187,9 @@ public class IdCanvas int alheight = av.alignment.getHeight(); if (av.hasHiddenColumns) + { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } int annotationHeight = 0; AnnotationLabels labels = null; @@ -200,7 +203,9 @@ public class IdCanvas int hgap = av.charHeight; if (av.scaleAboveWrapped) + { hgap += av.charHeight; + } int cHeight = alheight * av.charHeight + hgap @@ -220,7 +225,9 @@ public class IdCanvas setHiddenFont(i); } else + { gg.setFont(italic); + } SequenceI s = av.alignment.getSequenceAt(i); drawIdString(gg, s, i, 0, ypos); @@ -240,6 +247,7 @@ public class IdCanvas //Now draw the id strings //Now draw the id strings + SequenceI seq; for (int i = starty; i < endy; i++) { if (av.hasHiddenRows) @@ -247,23 +255,28 @@ public class IdCanvas setHiddenFont(i); } + seq = av.alignment.getSequenceAt(i); + if (seq == null) + { + continue; + } + // Selected sequence colours if ( (searchResults != null) && - searchResults.contains(av.alignment.getSequenceAt(i))) + searchResults.contains(seq)) { currentColor = Color.black; currentTextColor = Color.white; } else if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().getSequences(false).contains( - av.alignment.getSequenceAt(i))) + 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; } @@ -274,15 +287,15 @@ public class IdCanvas gg.setColor(currentTextColor); - String string = av.alignment.getSequenceAt(i).getDisplayId(av. - getShowJVSuffix()); - - gg.drawString(string, 0, + 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); + } } } } @@ -295,51 +308,76 @@ public class IdCanvas void drawMarker(int i, int starty, int yoffset) { - int hiddenIndex = av.adjustForHiddenSeqs(i); - int lastIndex = av.adjustForHiddenSeqs(i - 1); - int nextIndex = av.adjustForHiddenSeqs(i + 1); + 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); + boolean above = (nextIndex > hiddenIndex + 1); - gg.setColor(Color.blue); - if(below) + for (int j = 0; j < hSize; j++) + { + if (hseqs[j] != null) { - gg.fillPolygon(new int[] - {getSize().width- av.charHeight, - getSize().width- av.charHeight, - getSize().width}, - new int[] - { - (i - starty) * av.charHeight +yoffset, - (i - starty) * av.charHeight +yoffset+ av.charHeight / 4, - (i - starty) * av.charHeight+yoffset - }, 3); + if (j - 1 < hiddenIndex) + { + hiddenIndex++; + } + if (j - 1 < lastIndex) + { + lastIndex++; + } + if (j - 1 < nextIndex) + { + nextIndex++; + } } - if(above) - { - gg.fillPolygon(new int[] - {getSize().width- av.charHeight, - getSize().width - av.charHeight, - getSize().width }, - new int[] - { - (i - starty+1) * av.charHeight +yoffset, - (i - starty+1) * av.charHeight +yoffset- av.charHeight / 4, - (i - starty+1) * av.charHeight +yoffset - }, 3); + } - } + gg.setColor(Color.blue); + if (below) + { + gg.fillPolygon(new int[] + {getSize().width - av.charHeight, + getSize().width - av.charHeight, + getSize().width}, + 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[] + {getSize().width - av.charHeight, + getSize().width - av.charHeight, + getSize().width}, + 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) { - /* System.out.println(i+" "+av.alignment.getHeight()); - if (av.alignment.getSequenceAt(i).getHiddenSequences() != null) - gg.setFont(new Font(av.getFont().getName(), Font.BOLD, - av.getFont().getSize())); - else - gg.setFont(new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()));*/ + /* System.out.println(i+" "+av.alignment.getHeight()); + if (av.alignment.getSequenceAt(i).getHiddenSequences() != null) + gg.setFont(new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize())); + else + gg.setFont(new Font(av.getFont().getName(), Font.ITALIC, + av.getFont().getSize()));*/ } }