X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=c2a2ccbdab4bbf429c20c7c78e8720db4daa0e09;hb=80e3c4b6e17a6262ccbc193b9824ea3700a86f87;hp=a6219897200cb55a7b1cf036d8b93e2b8cbd4ff7;hpb=52402128d98c6744eb6348dd788fe6e8cd34575c;p=jalview.git diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java index a621989..c2a2ccb 100755 --- a/src/jalview/gui/SeqCanvas.java +++ b/src/jalview/gui/SeqCanvas.java @@ -21,11 +21,13 @@ package jalview.gui; import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.renderer.ScaleRenderer; import jalview.renderer.ScaleRenderer.ScaleMark; +import jalview.viewmodel.ViewportRanges; import java.awt.BasicStroke; import java.awt.BorderLayout; @@ -62,8 +64,6 @@ public class SeqCanvas extends JComponent AlignViewport av; - SearchResultsI searchResults = null; - boolean fastPaint = false; int LABEL_WEST; @@ -166,14 +166,17 @@ public class SeqCanvas extends JComponent if (av.hasHiddenColumns()) { - startx = av.getColumnSelection().adjustForHiddenColumns(startx); - endx = av.getColumnSelection().adjustForHiddenColumns(endx); + startx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(startx); + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); } int maxwidth = av.getAlignment().getWidth(); if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } // WEST SCALE @@ -225,7 +228,8 @@ public class SeqCanvas extends JComponent if (av.hasHiddenColumns()) { - endx = av.getColumnSelection().adjustForHiddenColumns(endx); + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); } SequenceI seq; @@ -281,10 +285,11 @@ public class SeqCanvas extends JComponent gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth, imgHeight, -horizontal * charWidth, -vertical * charHeight); - int sr = av.startRes; - int er = av.endRes; - int ss = av.startSeq; - int es = av.endSeq; + ViewportRanges ranges = av.getRanges(); + int sr = ranges.getStartRes(); + int er = ranges.getEndRes(); + int ss = ranges.getStartSeq(); + int es = ranges.getEndSeq(); int transX = 0; int transY = 0; @@ -302,22 +307,22 @@ public class SeqCanvas extends JComponent { ss = es - vertical; - if (ss < av.startSeq) + if (ss < ranges.getStartSeq()) { // ie scrolling too fast, more than a page at a time - ss = av.startSeq; + ss = ranges.getStartSeq(); } else { - transY = imgHeight - (vertical * charHeight); + transY = imgHeight - ((vertical + 1) * charHeight); } } else if (vertical < 0) { es = ss - vertical; - if (es > av.endSeq) + if (es > ranges.getEndSeq()) { - es = av.endSeq; + es = ranges.getEndSeq(); } } @@ -397,13 +402,15 @@ public class SeqCanvas extends JComponent gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, imgHeight); + ViewportRanges ranges = av.getRanges(); if (av.getWrapAlignment()) { - drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes); + drawWrappedPanel(gg, getWidth(), getHeight(), ranges.getStartRes()); } else { - drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); + drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(), + ranges.getStartSeq(), ranges.getEndSeq(), 0); } g.drawImage(lcimg, 0, 0, this); @@ -505,7 +512,7 @@ public class SeqCanvas extends JComponent av.setWrappedWidth(cWidth); - av.endRes = av.startRes + cWidth; + av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth); int endx; int ypos = hgap; @@ -513,7 +520,8 @@ public class SeqCanvas extends JComponent if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } while ((ypos <= canvasHeight) && (startRes < maxwidth)) @@ -551,11 +559,10 @@ public class SeqCanvas extends JComponent { g.setColor(Color.blue); int res; - for (int i = 0; i < av.getColumnSelection().getHiddenColumns() - .size(); i++) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + for (int i = 0; i < hidden.getHiddenRegions().size(); i++) { - res = av.getColumnSelection().findHiddenRegionPosition(i) - - startRes; + res = hidden.findHiddenRegionPosition(i) - startRes; if (res < 0 || res > endx - startRes) { @@ -586,7 +593,7 @@ public class SeqCanvas extends JComponent (int) clip.getBounds().getHeight()); } - drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); if (av.isShowAnnotation()) { @@ -652,7 +659,8 @@ public class SeqCanvas extends JComponent } else { - List regions = av.getColumnSelection().getHiddenColumns(); + List regions = av.getAlignment().getHiddenColumns() + .getHiddenRegions(); int screenY = 0; int blockStart = startRes; @@ -681,7 +689,7 @@ public class SeqCanvas extends JComponent g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1, 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1, - (endSeq - startSeq) * charHeight + offset); + (endSeq - startSeq + 1) * charHeight + offset); } g1.translate(-screenY * charWidth, 0); @@ -720,7 +728,7 @@ public class SeqCanvas extends JComponent // / First draw the sequences // /////////////////////////// - for (int i = startSeq; i < endSeq; i++) + for (int i = startSeq; i <= endSeq; i++) { nextSeq = av.getAlignment().getSequenceAt(i); if (nextSeq == null) @@ -735,15 +743,15 @@ public class SeqCanvas extends JComponent if (av.isShowSequenceFeatures()) { fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * charHeight)); + + ((i - startSeq) * charHeight), false); } // / Highlight search Results once all sequences have been drawn // //////////////////////////////////////////////////////// - if (searchResults != null) + if (av.hasSearchResults()) { - int[] visibleResults = searchResults.getResults(nextSeq, startRes, - endRes); + int[] visibleResults = av.getSearchResults().getResults(nextSeq, + startRes, endRes); if (visibleResults != null) { for (int r = 0; r < visibleResults.length; r += 2) @@ -804,7 +812,7 @@ public class SeqCanvas extends JComponent int top = -1; int bottom = -1; - for (i = startSeq; i < endSeq; i++) + for (i = startSeq; i <= endSeq; i++) { sx = (group.getStartRes() - startRes) * charWidth; sy = offset + ((i - startSeq) * charHeight); @@ -969,7 +977,7 @@ public class SeqCanvas extends JComponent { img = null; - searchResults = results; + av.setSearchResults(results); repaint(); }