X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=39382c54e31663feb9637b99423dd3dcf873d2ba;hb=14985603cea28569e295ddabb219da8034f1c7b2;hp=821136fa448053f3bcf9a0c327dc787aee04efcf;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java index 821136f..39382c5 100755 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,12 +21,14 @@ package jalview.appletgui; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; +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.AlignmentViewport; +import jalview.viewmodel.ViewportRanges; import java.awt.Color; import java.awt.FontMetrics; @@ -50,8 +52,6 @@ public class SeqCanvas extends Panel AlignViewport av; - SearchResults searchResults = null; - boolean fastPaint = false; int cursorX = 0; @@ -124,14 +124,17 @@ public class SeqCanvas extends Panel ypos += avcharHeight; 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 @@ -171,7 +174,8 @@ public class SeqCanvas extends Panel if (av.hasHiddenColumns()) { - endx = av.getColumnSelection().adjustForHiddenColumns(endx); + endx = av.getAlignment().getHiddenColumns() + .adjustForHiddenColumns(endx); } SequenceI seq; @@ -213,17 +217,19 @@ public class SeqCanvas extends Panel return; } + ViewportRanges ranges = av.getRanges(); + updateViewport(); // Its possible on certain browsers that the call to fastpaint // is faster than it can paint, so this check here catches // this possibility - if (lastsr + horizontal != av.startRes) + if (lastsr + horizontal != ranges.getStartRes()) { - horizontal = av.startRes - lastsr; + horizontal = ranges.getStartRes() - lastsr; } - lastsr = av.startRes; + lastsr = ranges.getStartRes(); fastPaint = true; gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth @@ -231,7 +237,9 @@ public class SeqCanvas extends Panel imgHeight - vertical * avcharHeight, -horizontal * avcharWidth, -vertical * avcharHeight); - int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0; + int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges + .getStartSeq(), es = ranges + .getEndSeq(), transX = 0, transY = 0; if (horizontal > 0) // scrollbar pulled right, image to the left { @@ -246,21 +254,23 @@ public class SeqCanvas extends Panel else if (vertical > 0) // scroll down { ss = es - vertical; - if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time + 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 * avcharHeight; + transY = imgHeight - ((vertical + 1) * avcharHeight); } } else if (vertical < 0) { es = ss - vertical; - if (es > av.endSeq) + if (es > ranges.getEndSeq()) { - es = av.endSeq; + es = ranges.getEndSeq(); } } @@ -331,13 +341,16 @@ public class SeqCanvas extends Panel gg.setColor(Color.white); gg.fillRect(0, 0, imgWidth, imgHeight); + ViewportRanges ranges = av.getRanges(); + if (av.getWrapAlignment()) { - drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); + drawWrappedPanel(gg, imgWidth, imgHeight, 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(img, 0, 0, this); @@ -423,7 +436,7 @@ public class SeqCanvas extends Panel av.setWrappedWidth(cWidth); - av.endRes = av.startRes + cWidth; + av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth); int endx; int ypos = hgap; @@ -432,7 +445,8 @@ public class SeqCanvas extends Panel if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .findColumnPosition(maxwidth) - 1; } while ((ypos <= canvasHeight) && (startRes < maxwidth)) @@ -466,12 +480,13 @@ public class SeqCanvas extends Panel } if (av.hasHiddenColumns() && av.getShowHiddenMarkers()) { + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); g.setColor(Color.blue); int res; - for (int i = 0; i < av.getColumnSelection().getHiddenColumns() + for (int i = 0; i < hidden.getHiddenRegions() .size(); i++) { - res = av.getColumnSelection().findHiddenRegionPosition(i) + res = hidden.findHiddenRegionPosition(i) - startRes; if (res < 0 || res > endx - startRes) @@ -493,7 +508,7 @@ public class SeqCanvas extends Panel g.setClip(0, 0, cWidth * avcharWidth, canvasHeight); } - drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); + drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos); g.setClip(null); if (av.isShowAnnotation()) @@ -550,7 +565,8 @@ public class SeqCanvas extends Panel if (av.hasHiddenColumns()) { - for (int[] region : av.getColumnSelection().getHiddenColumns()) + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + for (int[] region : hidden.getHiddenRegions()) { int hideStart = region[0]; int hideEnd = region[1]; @@ -572,7 +588,7 @@ public class SeqCanvas extends Panel g1.setColor(Color.blue); g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1, 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - - 1, (endSeq - startSeq) * avcharHeight + - 1, (endSeq - startSeq + 1) * avcharHeight + offset); } @@ -612,7 +628,7 @@ public class SeqCanvas extends Panel // / First draw the sequences // /////////////////////////// - for (int i = startSeq; i < endSeq; i++) + for (int i = startSeq; i <= endSeq; i++) { nextSeq = av.getAlignment().getSequenceAt(i); @@ -627,14 +643,15 @@ public class SeqCanvas extends Panel if (av.isShowSequenceFeatures()) { fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * avcharHeight)); + + ((i - startSeq) * avcharHeight), false); } // / Highlight search Results once all sequences have been drawn // //////////////////////////////////////////////////////// - if (searchResults != null) + if (av.hasSearchResults()) { - int[] visibleResults = searchResults.getResults(nextSeq, startRes, + int[] visibleResults = av.getSearchResults().getResults(nextSeq, + startRes, endRes); if (visibleResults != null) { @@ -695,7 +712,7 @@ public class SeqCanvas extends Panel int bottom = -1; int alHeight = av.getAlignment().getHeight() - 1; - for (i = startSeq; i < endSeq; i++) + for (i = startSeq; i <= endSeq; i++) { sx = (group.getStartRes() - startRes) * avcharWidth; sy = offset + ((i - startSeq) * avcharHeight); @@ -843,10 +860,9 @@ public class SeqCanvas extends Panel } } - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { - searchResults = results; - + av.setSearchResults(results); repaint(); }