From: Jim Procter Date: Fri, 23 Jan 2015 14:06:11 +0000 (+0000) Subject: Merge branch 'develop' into feature_29/JAL-1372_referenceseq X-Git-Tag: Jalview_2_9~108^2~6 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f58113903c158201e64b3db50cc6cd57a8db6ae6;p=jalview.git Merge branch 'develop' into feature_29/JAL-1372_referenceseq finessing between two branches where bugs are patched twice Conflicts: src/jalview/appletgui/ScalePanel.java src/jalview/appletgui/SeqCanvas.java src/jalview/datamodel/ColumnSelection.java --- f58113903c158201e64b3db50cc6cd57a8db6ae6 diff --cc src/jalview/appletgui/ScalePanel.java index f888e3a,bc5b3e7..2b6f37a --- a/src/jalview/appletgui/ScalePanel.java +++ b/src/jalview/appletgui/ScalePanel.java @@@ -108,7 -108,7 +108,7 @@@ public class ScalePanel extends Panel i }); pop.add(item); - if (av.getColumnSelection().hasHiddenColumns()) - if (av.getColumnSelection().getHiddenColumns().size() > 1) ++ if (av.getColumnSelection().hasManyHiddenColumns()) { item = new MenuItem(MessageManager.getString("action.reveal_all")); item.addActionListener(new ActionListener() diff --cc src/jalview/appletgui/SeqCanvas.java index 81e5dae,4b3cd1c..8dd6290 --- a/src/jalview/appletgui/SeqCanvas.java +++ b/src/jalview/appletgui/SeqCanvas.java @@@ -1,828 -1,836 +1,830 @@@ --/* -- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) -- * Copyright (C) 2014 The Jalview Authors -- * -- * This file is part of Jalview. -- * -- * Jalview is free software: you can redistribute it and/or -- * modify it under the terms of the GNU General Public License -- * as published by the Free Software Foundation, either version 3 -- * of the License, or (at your option) any later version. -- * -- * Jalview is distributed in the hope that it will be useful, but -- * WITHOUT ANY WARRANTY; without even the implied warranty -- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR -- * PURPOSE. See the GNU General Public License for more details. -- * -- * You should have received a copy of the GNU General Public License -- * along with Jalview. If not, see . -- * The Jalview Authors are detailed in the 'AUTHORS' file. -- */ --package jalview.appletgui; -- --import jalview.datamodel.AlignmentI; --import jalview.datamodel.SearchResults; --import jalview.datamodel.SequenceGroup; --import jalview.datamodel.SequenceI; -- --import java.awt.Color; --import java.awt.FontMetrics; --import java.awt.Graphics; --import java.awt.Image; --import java.awt.Panel; -- --public class SeqCanvas extends Panel --{ -- FeatureRenderer fr; -- -- SequenceRenderer sr; -- -- Image img; -- -- Graphics gg; -- -- int imgWidth; -- -- int imgHeight; -- -- AlignViewport av; -- -- SearchResults searchResults = null; -- -- boolean fastPaint = false; -- -- int cursorX = 0; -- -- int cursorY = 0; -- -- public SeqCanvas(AlignViewport av) -- { -- this.av = av; -- fr = new FeatureRenderer(av); -- sr = new SequenceRenderer(av); -- PaintRefresher.Register(this, av.getSequenceSetId()); -- } -- -- public AlignViewport getViewport() -- { -- return av; -- } -- -- public FeatureRenderer getFeatureRenderer() -- { -- return fr; -- } -- -- public SequenceRenderer getSequenceRenderer() -- { -- return sr; -- } -- -- void drawNorthScale(Graphics g, int startx, int endx, int ypos) -- { -- int scalestartx = startx - startx % 10 + 10; -- -- g.setColor(Color.black); -- -- // NORTH SCALE -- for (int i = scalestartx; i < endx; i += 10) -- { -- int value = i; -- if (av.hasHiddenColumns()) -- { -- value = av.getColumnSelection().adjustForHiddenColumns(value); -- } -- -- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth, -- ypos - (av.charHeight / 2)); -- -- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2), -- (ypos + 2) - (av.charHeight / 2), -- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), -- ypos - 2); -- } -- } -- -- void drawWestScale(Graphics g, int startx, int endx, int ypos) -- { -- FontMetrics fm = getFontMetrics(av.getFont()); -- ypos += av.charHeight; -- if (av.hasHiddenColumns()) -- { -- startx = av.getColumnSelection().adjustForHiddenColumns(startx); -- endx = av.getColumnSelection().adjustForHiddenColumns(endx); -- } -- -- int maxwidth = av.getAlignment().getWidth(); -- if (av.hasHiddenColumns()) -- { -- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; -- } -- -- // WEST SCALE -- for (int i = 0; i < av.getAlignment().getHeight(); i++) -- { -- SequenceI seq = av.getAlignment().getSequenceAt(i); -- int index = startx; -- int value = -1; -- -- while (index < endx) -- { -- if (jalview.util.Comparison.isGap(seq.getCharAt(index))) -- { -- index++; -- -- continue; -- } -- -- value = av.getAlignment().getSequenceAt(i).findPosition(index); -- -- break; -- } -- -- if (value != -1) -- { -- int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) -- - av.charWidth / 2; -- g.drawString(value + "", x, (ypos + (i * av.charHeight)) -- - (av.charHeight / 5)); -- } -- } -- } -- -- void drawEastScale(Graphics g, int startx, int endx, int ypos) -- { -- ypos += av.charHeight; -- -- if (av.hasHiddenColumns()) -- { -- endx = av.getColumnSelection().adjustForHiddenColumns(endx); -- } -- -- SequenceI seq; -- // EAST SCALE -- for (int i = 0; i < av.getAlignment().getHeight(); i++) -- { -- seq = av.getAlignment().getSequenceAt(i); -- int index = endx; -- int value = -1; -- -- while (index > startx) -- { -- if (jalview.util.Comparison.isGap(seq.getCharAt(index))) -- { -- index--; -- -- continue; -- } -- -- value = seq.findPosition(index); -- -- break; -- } -- -- if (value != -1) -- { -- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight)) -- - (av.charHeight / 5)); -- } -- } -- } -- -- int lastsr = 0; -- -- void fastPaint(int horizontal, int vertical) -- { -- if (fastPaint || gg == null) -- { -- return; -- } -- -- // 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) -- { -- horizontal = av.startRes - lastsr; -- } -- -- lastsr = av.startRes; -- -- fastPaint = true; -- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight, -- imgWidth - horizontal * av.charWidth, imgHeight - vertical -- * av.charHeight, -horizontal * av.charWidth, -vertical -- * av.charHeight); -- -- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0; -- -- if (horizontal > 0) // scrollbar pulled right, image to the left -- { -- transX = (er - sr - horizontal) * av.charWidth; -- sr = er - horizontal; -- } -- else if (horizontal < 0) -- { -- er = sr - horizontal; -- } -- -- else if (vertical > 0) // scroll down -- { -- ss = es - vertical; -- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time -- { -- ss = av.startSeq; -- } -- else -- { -- transY = imgHeight - vertical * av.charHeight; -- } -- } -- else if (vertical < 0) -- { -- es = ss - vertical; -- if (es > av.endSeq) -- { -- es = av.endSeq; -- } -- } -- -- gg.translate(transX, transY); -- -- drawPanel(gg, sr, er, ss, es, 0); -- gg.translate(-transX, -transY); -- -- repaint(); -- -- } -- -- /** -- * Definitions of startx and endx (hopefully): SMJS This is what I'm working -- * towards! startx is the first residue (starting at 0) to display. endx is -- * the last residue to display (starting at 0). starty is the first sequence -- * to display (starting at 0). endy is the last sequence to display (starting -- * at 0). NOTE 1: The av limits are set in setFont in this class and in the -- * adjustment listener in SeqPanel when the scrollbars move. -- */ -- public void update(Graphics g) -- { -- paint(g); -- } -- -- public void paint(Graphics g) -- { -- -- if (img != null -- && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g -- .getClipBounds().height))) -- { -- g.drawImage(img, 0, 0, this); -- fastPaint = false; -- return; -- } -- -- if (fastPaint) -- { -- g.drawImage(img, 0, 0, this); -- fastPaint = false; -- return; -- } -- -- // this draws the whole of the alignment -- imgWidth = this.getSize().width; -- imgHeight = this.getSize().height; -- -- imgWidth -= imgWidth % av.charWidth; -- imgHeight -= imgHeight % av.charHeight; -- -- if (imgWidth < 1 || imgHeight < 1) -- { -- return; -- } -- -- if (img == null || imgWidth != img.getWidth(this) -- || imgHeight != img.getHeight(this)) -- { -- img = createImage(imgWidth, imgHeight); -- gg = img.getGraphics(); -- gg.setFont(av.getFont()); -- } -- -- gg.setColor(Color.white); -- gg.fillRect(0, 0, imgWidth, imgHeight); -- -- if (av.getWrapAlignment()) -- { -- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); -- } -- else -- { -- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); -- } -- -- g.drawImage(img, 0, 0, this); -- -- } -- -- int LABEL_WEST, LABEL_EAST; -- -- public int getWrappedCanvasWidth(int cwidth) -- { -- cwidth -= cwidth % av.charWidth; -- -- FontMetrics fm = getFontMetrics(av.getFont()); -- -- LABEL_EAST = 0; -- LABEL_WEST = 0; -- -- if (av.scaleRightWrapped) -- { -- LABEL_EAST = fm.stringWidth(getMask()); -- } -- -- if (av.scaleLeftWrapped) -- { -- LABEL_WEST = fm.stringWidth(getMask()); -- } -- -- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; -- } -- -- /** -- * Generates a string of zeroes. -- * -- * @return String -- */ -- String getMask() -- { -- String mask = "0"; -- int maxWidth = 0; -- int tmp; -- AlignmentI alignment = av.getAlignment(); -- for (int i = 0; i < alignment.getHeight(); i++) -- { -- tmp = alignment.getSequenceAt(i).getEnd(); -- if (tmp > maxWidth) -- { -- maxWidth = tmp; -- } -- } -- -- for (int i = maxWidth; i > 0; i /= 10) -- { -- mask += "0"; -- } -- return mask; -- } -- -- public void drawWrappedPanel(Graphics g, int canvasWidth, -- int canvasHeight, int startRes) -- { -- AlignmentI al = av.getAlignment(); -- -- FontMetrics fm = getFontMetrics(av.getFont()); -- -- if (av.scaleRightWrapped) -- { -- LABEL_EAST = fm.stringWidth(getMask()); -- } -- -- if (av.scaleLeftWrapped) -- { -- LABEL_WEST = fm.stringWidth(getMask()); -- } -- -- int hgap = av.charHeight; -- if (av.scaleAboveWrapped) -- { -- hgap += av.charHeight; -- } -- -- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; -- int cHeight = av.getAlignment().getHeight() * av.charHeight; -- -- av.setWrappedWidth(cWidth); -- -- av.endRes = av.startRes + cWidth; -- -- int endx; -- int ypos = hgap; -- -- int maxwidth = av.getAlignment().getWidth() - 1; -- -- if (av.hasHiddenColumns()) -- { -- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; -- } -- -- while ((ypos <= canvasHeight) && (startRes < maxwidth)) -- { -- endx = startRes + cWidth - 1; -- -- if (endx > maxwidth) -- { -- endx = maxwidth; -- } -- -- g.setColor(Color.black); -- -- if (av.scaleLeftWrapped) -- { -- drawWestScale(g, startRes, endx, ypos); -- } -- -- if (av.scaleRightWrapped) -- { -- g.translate(canvasWidth - LABEL_EAST, 0); -- drawEastScale(g, startRes, endx, ypos); -- g.translate(-(canvasWidth - LABEL_EAST), 0); -- } -- -- g.translate(LABEL_WEST, 0); -- -- if (av.scaleAboveWrapped) -- { -- drawNorthScale(g, startRes, endx, ypos); -- } -- if (av.hasHiddenColumns() && av.showHiddenMarkers) -- { -- g.setColor(Color.blue); -- int res; -- for (int i = 0; i < av.getColumnSelection().getHiddenColumns() -- .size(); i++) -- { -- res = av.getColumnSelection().findHiddenRegionPosition(i) -- - startRes; -- -- if (res < 0 || res > endx - startRes) -- { -- continue; -- } -- -- gg.fillPolygon(new int[] -- { res * av.charWidth - av.charHeight / 4, -- res * av.charWidth + av.charHeight / 4, res * av.charWidth }, -- new int[] -- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2), -- ypos - (av.charHeight / 2) + 8 }, 3); -- -- } -- } -- -- if (g.getClip() == null) -- { -- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); -- } -- -- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); -- g.setClip(null); -- -- if (av.showAnnotation) -- { -- g.translate(0, cHeight + ypos + 4); -- if (annotations == null) -- { -- annotations = new AnnotationPanel(av); -- } -- -- annotations.drawComponent(g, startRes, endx + 1); -- g.translate(0, -cHeight - ypos - 4); -- } -- g.translate(-LABEL_WEST, 0); -- -- ypos += cHeight + getAnnotationHeight() + hgap; -- -- startRes += cWidth; -- } -- -- } -- -- AnnotationPanel annotations; -- -- int getAnnotationHeight() -- { -- if (!av.showAnnotation) -- { -- return 0; -- } -- -- if (annotations == null) -- { -- annotations = new AnnotationPanel(av); -- } -- -- return annotations.adjustPanelHeight(); -- } -- -- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, -- int endSeq, int offset) -- { - if (!av.hasHiddenColumns()) - { - draw(g1, startRes, endRes, startSeq, endSeq, offset); - } - else - { - java.util.List regions = av.getColumnSelection() - .getHiddenColumns(); -- - int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; -- - for (int i = 0; i < regions.size(); i++) - { - int[] region = regions.get(i); - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; - - g1.translate(screenY * av.charWidth, 0); - - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - - if (av.getShowHiddenMarkers()) - { - g1.setColor(Color.blue); - g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) * av.charWidth - - 1, (endSeq - startSeq) * av.charHeight + offset); - } - - g1.translate(-screenY * av.charWidth, 0); - screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - } - - if (screenY <= (endRes - startRes)) - { - blockEnd = blockStart + (endRes - startRes) - screenY; - g1.translate(screenY * av.charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - - g1.translate(-screenY * av.charWidth, 0); - } - } - - } - - // int startRes, int endRes, int startSeq, int endSeq, int x, int y, - // int x1, int x2, int y1, int y2, int startx, int starty, - void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, - int offset) - { - g.setFont(av.getFont()); - sr.prepare(g, av.renderGaps); - - SequenceI nextSeq; - - // / First draw the sequences - // /////////////////////////// - for (int i = startSeq; i < endSeq; i++) - { - nextSeq = av.getAlignment().getSequenceAt(i); - - if (nextSeq == null) - { - continue; - } - - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), - startRes, endRes, offset + ((i - startSeq) * av.charHeight)); - - if (av.isShowSequenceFeatures()) - { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * av.charHeight)); - } - - // / Highlight search Results once all sequences have been drawn - // //////////////////////////////////////////////////////// - if (searchResults != null) - { - int[] visibleResults = searchResults.getResults(nextSeq, startRes, - endRes); - if (visibleResults != null) - { - for (int r = 0; r < visibleResults.length; r += 2) - { - sr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * av.charWidth, offset - + ((i - startSeq) * av.charHeight)); - } - } - } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - sr.drawCursor(nextSeq, cursorX, - (cursorX - startRes) * av.charWidth, offset - + ((i - startSeq) * av.charHeight)); - } - } - - if (av.getSelectionGroup() != null - || av.getAlignment().getGroups().size() > 0) - { - drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); - } - - } - - void drawGroupsBoundaries(Graphics g, int startRes, int endRes, - int startSeq, int endSeq, int offset) - { - // - // /////////////////////////////////// - // Now outline any areas if necessary - // /////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - - int sx = -1; - int sy = -1; - int ex = -1; - int groupIndex = -1; - - if ((group == null) && (av.getAlignment().getGroups().size() > 0)) - { - group = av.getAlignment().getGroups().get(0); - groupIndex = 0; - } - - if (group != null) - { - do - { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; - int alHeight = av.getAlignment().getHeight() - 1; - - for (i = startSeq; i < endSeq; i++) - { - sx = (group.getStartRes() - startRes) * av.charWidth; - sy = offset + ((i - startSeq) * av.charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; - - if (sx + ex < 0 || sx > imgWidth) - { - continue; - } - - if ((sx <= (endRes - startRes) * av.charWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) - && (i >= alHeight || !group.getSequences(null) - .contains( - av.getAlignment().getSequenceAt(i + 1)))) - { - bottom = sy + av.charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - if (group == av.getSelectionGroup()) - { - g.setColor(Color.red); - } - else - { - g.setColor(group.getOutlineColour()); - } - } - } - else - { - if (inGroup) - { - if (sx >= 0 && sx < imgWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < imgWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - { - ex = imgWidth; - } - - else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) - { - ex = (endRes - startRes + 1) * av.charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - inGroup = false; - } - } - } - - if (inGroup) - { - sy = offset + ((i - startSeq) * av.charHeight); - if (sx >= 0 && sx < imgWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < imgWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - { - ex = imgWidth; - } - else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) - { - ex = (endRes - startRes + 1) * av.charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; - } - - inGroup = false; - } - - groupIndex++; - - if (groupIndex >= av.getAlignment().getGroups().size()) - { - break; - } - - group = av.getAlignment().getGroups() - .get(groupIndex); - } while (groupIndex < av.getAlignment().getGroups().size()); - - } - } - - public void highlightSearchResults(SearchResults results) - { - searchResults = results; - - repaint(); - } - - } - if (!av.hasHiddenColumns()) - { - draw(g1, startRes, endRes, startSeq, endSeq, offset); - } - else - { - - - - int screenY = 0; - int blockStart = startRes; - int blockEnd = endRes; - - if (av.getColumnSelection() != null - && av.getColumnSelection().getHiddenColumns() != null) - { - java.util.Vector regions = av.getColumnSelection() - .getHiddenColumns(); - - for (int i = 0; i < regions.size(); i++) - { - int[] region = (int[]) regions.elementAt(i); - int hideStart = region[0]; - int hideEnd = region[1]; - - if (hideStart <= blockStart) - { - blockStart += (hideEnd - hideStart) + 1; - continue; - } - - blockEnd = hideStart - 1; - - g1.translate(screenY * av.charWidth, 0); - - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - - if (av.getShowHiddenMarkers()) - { - g1.setColor(Color.blue); - g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, - 0 + offset, (blockEnd - blockStart + 1) * av.charWidth - - 1, (endSeq - startSeq) * av.charHeight + offset); - } - - g1.translate(-screenY * av.charWidth, 0); - screenY += blockEnd - blockStart + 1; - blockStart = hideEnd + 1; - } - } - if (screenY <= (endRes - startRes)) - { - blockEnd = blockStart + (endRes - startRes) - screenY; - g1.translate(screenY * av.charWidth, 0); - draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); - - g1.translate(-screenY * av.charWidth, 0); - } - } - - } - - // int startRes, int endRes, int startSeq, int endSeq, int x, int y, - // int x1, int x2, int y1, int y2, int startx, int starty, - void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, - int offset) - { - g.setFont(av.getFont()); - sr.prepare(g, av.renderGaps); - - SequenceI nextSeq; - - // / First draw the sequences - // /////////////////////////// - for (int i = startSeq; i < endSeq; i++) - { - nextSeq = av.getAlignment().getSequenceAt(i); - - if (nextSeq == null) - { - continue; - } - - sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), - startRes, endRes, offset + ((i - startSeq) * av.charHeight)); - - if (av.isShowSequenceFeatures()) - { - fr.drawSequence(g, nextSeq, startRes, endRes, offset - + ((i - startSeq) * av.charHeight)); - } - - // / Highlight search Results once all sequences have been drawn - // //////////////////////////////////////////////////////// - if (searchResults != null) - { - int[] visibleResults = searchResults.getResults(nextSeq, startRes, - endRes); - if (visibleResults != null) - { - for (int r = 0; r < visibleResults.length; r += 2) - { - sr.drawHighlightedText(nextSeq, visibleResults[r], - visibleResults[r + 1], (visibleResults[r] - startRes) - * av.charWidth, offset - + ((i - startSeq) * av.charHeight)); - } - } - } - - if (av.cursorMode && cursorY == i && cursorX >= startRes - && cursorX <= endRes) - { - sr.drawCursor(nextSeq, cursorX, - (cursorX - startRes) * av.charWidth, offset - + ((i - startSeq) * av.charHeight)); - } - } - - if (av.getSelectionGroup() != null - || av.getAlignment().getGroups().size() > 0) - { - drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); - } - - } - - void drawGroupsBoundaries(Graphics g, int startRes, int endRes, - int startSeq, int endSeq, int offset) - { - // - // /////////////////////////////////// - // Now outline any areas if necessary - // /////////////////////////////////// - SequenceGroup group = av.getSelectionGroup(); - - int sx = -1; - int sy = -1; - int ex = -1; - int groupIndex = -1; - - if ((group == null) && (av.getAlignment().getGroups().size() > 0)) - { - group = av.getAlignment().getGroups().get(0); - groupIndex = 0; - } - - if (group != null) - { - do - { - int oldY = -1; - int i = 0; - boolean inGroup = false; - int top = -1; - int bottom = -1; - int alHeight = av.getAlignment().getHeight() - 1; - - for (i = startSeq; i < endSeq; i++) - { - sx = (group.getStartRes() - startRes) * av.charWidth; - sy = offset + ((i - startSeq) * av.charHeight); - ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; - - if (sx + ex < 0 || sx > imgWidth) - { - continue; - } - - if ((sx <= (endRes - startRes) * av.charWidth) - && group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i))) - { - if ((bottom == -1) - && (i >= alHeight || !group.getSequences(null) - .contains( - av.getAlignment().getSequenceAt(i + 1)))) - { - bottom = sy + av.charHeight; - } - - if (!inGroup) - { - if (((top == -1) && (i == 0)) - || !group.getSequences(null).contains( - av.getAlignment().getSequenceAt(i - 1))) - { - top = sy; - } - - oldY = sy; - inGroup = true; - - if (group == av.getSelectionGroup()) - { - g.setColor(Color.red); - } - else - { - g.setColor(group.getOutlineColour()); - } - } - } - else - { - if (inGroup) - { - if (sx >= 0 && sx < imgWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < imgWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - { - ex = imgWidth; - } - - else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) - { - ex = (endRes - startRes + 1) * av.charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom, sx + ex, bottom); - bottom = -1; - } - - inGroup = false; - } - } - } - - if (inGroup) - { - sy = offset + ((i - startSeq) * av.charHeight); - if (sx >= 0 && sx < imgWidth) - { - g.drawLine(sx, oldY, sx, sy); - } - - if (sx + ex < imgWidth) - { - g.drawLine(sx + ex, oldY, sx + ex, sy); - } - - if (sx < 0) - { - ex += sx; - sx = 0; - } - - if (sx + ex > imgWidth) - { - ex = imgWidth; - } - else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) - { - ex = (endRes - startRes + 1) * av.charWidth; - } - - if (top != -1) - { - g.drawLine(sx, top, sx + ex, top); - top = -1; - } - - if (bottom != -1) - { - g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); - bottom = -1; - } - - inGroup = false; - } - - groupIndex++; - - if (groupIndex >= av.getAlignment().getGroups().size()) - { - break; - } - - group = av.getAlignment().getGroups() - .get(groupIndex); - } while (groupIndex < av.getAlignment().getGroups().size()); - - } - } - - public void highlightSearchResults(SearchResults results) - { - searchResults = results; - - repaint(); - } - -} ++/* ++ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) ++ * Copyright (C) 2014 The Jalview Authors ++ * ++ * This file is part of Jalview. ++ * ++ * Jalview is free software: you can redistribute it and/or ++ * modify it under the terms of the GNU General Public License ++ * as published by the Free Software Foundation, either version 3 ++ * of the License, or (at your option) any later version. ++ * ++ * Jalview is distributed in the hope that it will be useful, but ++ * WITHOUT ANY WARRANTY; without even the implied warranty ++ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR ++ * PURPOSE. See the GNU General Public License for more details. ++ * ++ * You should have received a copy of the GNU General Public License ++ * along with Jalview. If not, see . ++ * The Jalview Authors are detailed in the 'AUTHORS' file. ++ */ ++package jalview.appletgui; ++ ++import jalview.datamodel.AlignmentI; ++import jalview.datamodel.SearchResults; ++import jalview.datamodel.SequenceGroup; ++import jalview.datamodel.SequenceI; ++ ++import java.awt.Color; ++import java.awt.FontMetrics; ++import java.awt.Graphics; ++import java.awt.Image; ++import java.awt.Panel; ++ ++public class SeqCanvas extends Panel ++{ ++ FeatureRenderer fr; ++ ++ SequenceRenderer sr; ++ ++ Image img; ++ ++ Graphics gg; ++ ++ int imgWidth; ++ ++ int imgHeight; ++ ++ AlignViewport av; ++ ++ SearchResults searchResults = null; ++ ++ boolean fastPaint = false; ++ ++ int cursorX = 0; ++ ++ int cursorY = 0; ++ ++ public SeqCanvas(AlignViewport av) ++ { ++ this.av = av; ++ fr = new FeatureRenderer(av); ++ sr = new SequenceRenderer(av); ++ PaintRefresher.Register(this, av.getSequenceSetId()); ++ } ++ ++ public AlignViewport getViewport() ++ { ++ return av; ++ } ++ ++ public FeatureRenderer getFeatureRenderer() ++ { ++ return fr; ++ } ++ ++ public SequenceRenderer getSequenceRenderer() ++ { ++ return sr; ++ } ++ ++ void drawNorthScale(Graphics g, int startx, int endx, int ypos) ++ { ++ int scalestartx = startx - startx % 10 + 10; ++ ++ g.setColor(Color.black); ++ ++ // NORTH SCALE ++ for (int i = scalestartx; i < endx; i += 10) ++ { ++ int value = i; ++ if (av.hasHiddenColumns()) ++ { ++ value = av.getColumnSelection().adjustForHiddenColumns(value); ++ } ++ ++ g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth, ++ ypos - (av.charHeight / 2)); ++ ++ g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ++ (ypos + 2) - (av.charHeight / 2), ++ ((i - startx - 1) * av.charWidth) + (av.charWidth / 2), ++ ypos - 2); ++ } ++ } ++ ++ void drawWestScale(Graphics g, int startx, int endx, int ypos) ++ { ++ FontMetrics fm = getFontMetrics(av.getFont()); ++ ypos += av.charHeight; ++ if (av.hasHiddenColumns()) ++ { ++ startx = av.getColumnSelection().adjustForHiddenColumns(startx); ++ endx = av.getColumnSelection().adjustForHiddenColumns(endx); ++ } ++ ++ int maxwidth = av.getAlignment().getWidth(); ++ if (av.hasHiddenColumns()) ++ { ++ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; ++ } ++ ++ // WEST SCALE ++ for (int i = 0; i < av.getAlignment().getHeight(); i++) ++ { ++ SequenceI seq = av.getAlignment().getSequenceAt(i); ++ int index = startx; ++ int value = -1; ++ ++ while (index < endx) ++ { ++ if (jalview.util.Comparison.isGap(seq.getCharAt(index))) ++ { ++ index++; ++ ++ continue; ++ } ++ ++ value = av.getAlignment().getSequenceAt(i).findPosition(index); ++ ++ break; ++ } ++ ++ if (value != -1) ++ { ++ int x = LABEL_WEST - fm.stringWidth(String.valueOf(value)) ++ - av.charWidth / 2; ++ g.drawString(value + "", x, (ypos + (i * av.charHeight)) ++ - (av.charHeight / 5)); ++ } ++ } ++ } ++ ++ void drawEastScale(Graphics g, int startx, int endx, int ypos) ++ { ++ ypos += av.charHeight; ++ ++ if (av.hasHiddenColumns()) ++ { ++ endx = av.getColumnSelection().adjustForHiddenColumns(endx); ++ } ++ ++ SequenceI seq; ++ // EAST SCALE ++ for (int i = 0; i < av.getAlignment().getHeight(); i++) ++ { ++ seq = av.getAlignment().getSequenceAt(i); ++ int index = endx; ++ int value = -1; ++ ++ while (index > startx) ++ { ++ if (jalview.util.Comparison.isGap(seq.getCharAt(index))) ++ { ++ index--; ++ ++ continue; ++ } ++ ++ value = seq.findPosition(index); ++ ++ break; ++ } ++ ++ if (value != -1) ++ { ++ g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight)) ++ - (av.charHeight / 5)); ++ } ++ } ++ } ++ ++ int lastsr = 0; ++ ++ void fastPaint(int horizontal, int vertical) ++ { ++ if (fastPaint || gg == null) ++ { ++ return; ++ } ++ ++ // 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) ++ { ++ horizontal = av.startRes - lastsr; ++ } ++ ++ lastsr = av.startRes; ++ ++ fastPaint = true; ++ gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight, ++ imgWidth - horizontal * av.charWidth, imgHeight - vertical ++ * av.charHeight, -horizontal * av.charWidth, -vertical ++ * av.charHeight); ++ ++ int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0; ++ ++ if (horizontal > 0) // scrollbar pulled right, image to the left ++ { ++ transX = (er - sr - horizontal) * av.charWidth; ++ sr = er - horizontal; ++ } ++ else if (horizontal < 0) ++ { ++ er = sr - horizontal; ++ } ++ ++ else if (vertical > 0) // scroll down ++ { ++ ss = es - vertical; ++ if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time ++ { ++ ss = av.startSeq; ++ } ++ else ++ { ++ transY = imgHeight - vertical * av.charHeight; ++ } ++ } ++ else if (vertical < 0) ++ { ++ es = ss - vertical; ++ if (es > av.endSeq) ++ { ++ es = av.endSeq; ++ } ++ } ++ ++ gg.translate(transX, transY); ++ ++ drawPanel(gg, sr, er, ss, es, 0); ++ gg.translate(-transX, -transY); ++ ++ repaint(); ++ ++ } ++ ++ /** ++ * Definitions of startx and endx (hopefully): SMJS This is what I'm working ++ * towards! startx is the first residue (starting at 0) to display. endx is ++ * the last residue to display (starting at 0). starty is the first sequence ++ * to display (starting at 0). endy is the last sequence to display (starting ++ * at 0). NOTE 1: The av limits are set in setFont in this class and in the ++ * adjustment listener in SeqPanel when the scrollbars move. ++ */ ++ public void update(Graphics g) ++ { ++ paint(g); ++ } ++ ++ public void paint(Graphics g) ++ { ++ ++ if (img != null ++ && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g ++ .getClipBounds().height))) ++ { ++ g.drawImage(img, 0, 0, this); ++ fastPaint = false; ++ return; ++ } ++ ++ if (fastPaint) ++ { ++ g.drawImage(img, 0, 0, this); ++ fastPaint = false; ++ return; ++ } ++ ++ // this draws the whole of the alignment ++ imgWidth = this.getSize().width; ++ imgHeight = this.getSize().height; ++ ++ imgWidth -= imgWidth % av.charWidth; ++ imgHeight -= imgHeight % av.charHeight; ++ ++ if (imgWidth < 1 || imgHeight < 1) ++ { ++ return; ++ } ++ ++ if (img == null || imgWidth != img.getWidth(this) ++ || imgHeight != img.getHeight(this)) ++ { ++ img = createImage(imgWidth, imgHeight); ++ gg = img.getGraphics(); ++ gg.setFont(av.getFont()); ++ } ++ ++ gg.setColor(Color.white); ++ gg.fillRect(0, 0, imgWidth, imgHeight); ++ ++ if (av.getWrapAlignment()) ++ { ++ drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes); ++ } ++ else ++ { ++ drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0); ++ } ++ ++ g.drawImage(img, 0, 0, this); ++ ++ } ++ ++ int LABEL_WEST, LABEL_EAST; ++ ++ public int getWrappedCanvasWidth(int cwidth) ++ { ++ cwidth -= cwidth % av.charWidth; ++ ++ FontMetrics fm = getFontMetrics(av.getFont()); ++ ++ LABEL_EAST = 0; ++ LABEL_WEST = 0; ++ ++ if (av.scaleRightWrapped) ++ { ++ LABEL_EAST = fm.stringWidth(getMask()); ++ } ++ ++ if (av.scaleLeftWrapped) ++ { ++ LABEL_WEST = fm.stringWidth(getMask()); ++ } ++ ++ return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth; ++ } ++ ++ /** ++ * Generates a string of zeroes. ++ * ++ * @return String ++ */ ++ String getMask() ++ { ++ String mask = "0"; ++ int maxWidth = 0; ++ int tmp; ++ AlignmentI alignment = av.getAlignment(); ++ for (int i = 0; i < alignment.getHeight(); i++) ++ { ++ tmp = alignment.getSequenceAt(i).getEnd(); ++ if (tmp > maxWidth) ++ { ++ maxWidth = tmp; ++ } ++ } ++ ++ for (int i = maxWidth; i > 0; i /= 10) ++ { ++ mask += "0"; ++ } ++ return mask; ++ } ++ ++ public void drawWrappedPanel(Graphics g, int canvasWidth, ++ int canvasHeight, int startRes) ++ { ++ AlignmentI al = av.getAlignment(); ++ ++ FontMetrics fm = getFontMetrics(av.getFont()); ++ ++ if (av.scaleRightWrapped) ++ { ++ LABEL_EAST = fm.stringWidth(getMask()); ++ } ++ ++ if (av.scaleLeftWrapped) ++ { ++ LABEL_WEST = fm.stringWidth(getMask()); ++ } ++ ++ int hgap = av.charHeight; ++ if (av.scaleAboveWrapped) ++ { ++ hgap += av.charHeight; ++ } ++ ++ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth; ++ int cHeight = av.getAlignment().getHeight() * av.charHeight; ++ ++ av.setWrappedWidth(cWidth); ++ ++ av.endRes = av.startRes + cWidth; ++ ++ int endx; ++ int ypos = hgap; ++ ++ int maxwidth = av.getAlignment().getWidth() - 1; ++ ++ if (av.hasHiddenColumns()) ++ { ++ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; ++ } ++ ++ while ((ypos <= canvasHeight) && (startRes < maxwidth)) ++ { ++ endx = startRes + cWidth - 1; ++ ++ if (endx > maxwidth) ++ { ++ endx = maxwidth; ++ } ++ ++ g.setColor(Color.black); ++ ++ if (av.scaleLeftWrapped) ++ { ++ drawWestScale(g, startRes, endx, ypos); ++ } ++ ++ if (av.scaleRightWrapped) ++ { ++ g.translate(canvasWidth - LABEL_EAST, 0); ++ drawEastScale(g, startRes, endx, ypos); ++ g.translate(-(canvasWidth - LABEL_EAST), 0); ++ } ++ ++ g.translate(LABEL_WEST, 0); ++ ++ if (av.scaleAboveWrapped) ++ { ++ drawNorthScale(g, startRes, endx, ypos); ++ } ++ if (av.hasHiddenColumns() && av.showHiddenMarkers) ++ { ++ g.setColor(Color.blue); ++ int res; ++ for (int i = 0; i < av.getColumnSelection().getHiddenColumns() ++ .size(); i++) ++ { ++ res = av.getColumnSelection().findHiddenRegionPosition(i) ++ - startRes; ++ ++ if (res < 0 || res > endx - startRes) ++ { ++ continue; ++ } ++ ++ gg.fillPolygon(new int[] ++ { res * av.charWidth - av.charHeight / 4, ++ res * av.charWidth + av.charHeight / 4, res * av.charWidth }, ++ new int[] ++ { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2), ++ ypos - (av.charHeight / 2) + 8 }, 3); ++ ++ } ++ } ++ ++ if (g.getClip() == null) ++ { ++ g.setClip(0, 0, cWidth * av.charWidth, canvasHeight); ++ } ++ ++ drawPanel(g, startRes, endx, 0, al.getHeight(), ypos); ++ g.setClip(null); ++ ++ if (av.showAnnotation) ++ { ++ g.translate(0, cHeight + ypos + 4); ++ if (annotations == null) ++ { ++ annotations = new AnnotationPanel(av); ++ } ++ ++ annotations.drawComponent(g, startRes, endx + 1); ++ g.translate(0, -cHeight - ypos - 4); ++ } ++ g.translate(-LABEL_WEST, 0); ++ ++ ypos += cHeight + getAnnotationHeight() + hgap; ++ ++ startRes += cWidth; ++ } ++ ++ } ++ ++ AnnotationPanel annotations; ++ ++ int getAnnotationHeight() ++ { ++ if (!av.showAnnotation) ++ { ++ return 0; ++ } ++ ++ if (annotations == null) ++ { ++ annotations = new AnnotationPanel(av); ++ } ++ ++ return annotations.adjustPanelHeight(); ++ } ++ ++ void drawPanel(Graphics g1, int startRes, int endRes, int startSeq, ++ int endSeq, int offset) ++ { ++ ++ ++ if (!av.hasHiddenColumns()) ++ { ++ draw(g1, startRes, endRes, startSeq, endSeq, offset); ++ } ++ else ++ { ++ ++ int screenY = 0; ++ int blockStart = startRes; ++ int blockEnd = endRes; ++ ++ if (av.hasHiddenColumns()) ++ { ++ for (int[] region : av.getColumnSelection().getHiddenColumns()) ++ { ++ int hideStart = region[0]; ++ int hideEnd = region[1]; ++ ++ if (hideStart <= blockStart) ++ { ++ blockStart += (hideEnd - hideStart) + 1; ++ continue; ++ } ++ ++ blockEnd = hideStart - 1; ++ ++ g1.translate(screenY * av.charWidth, 0); ++ ++ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); ++ ++ if (av.getShowHiddenMarkers()) ++ { ++ g1.setColor(Color.blue); ++ g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1, ++ 0 + offset, (blockEnd - blockStart + 1) * av.charWidth ++ - 1, (endSeq - startSeq) * av.charHeight ++ + offset); ++ } ++ ++ g1.translate(-screenY * av.charWidth, 0); ++ screenY += blockEnd - blockStart + 1; ++ blockStart = hideEnd + 1; ++ } ++ } ++ if (screenY <= (endRes - startRes)) ++ { ++ blockEnd = blockStart + (endRes - startRes) - screenY; ++ g1.translate(screenY * av.charWidth, 0); ++ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset); ++ ++ g1.translate(-screenY * av.charWidth, 0); ++ } ++ } ++ ++ } ++ ++ // int startRes, int endRes, int startSeq, int endSeq, int x, int y, ++ // int x1, int x2, int y1, int y2, int startx, int starty, ++ void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq, ++ int offset) ++ { ++ g.setFont(av.getFont()); ++ sr.prepare(g, av.renderGaps); ++ ++ SequenceI nextSeq; ++ ++ // / First draw the sequences ++ // /////////////////////////// ++ for (int i = startSeq; i < endSeq; i++) ++ { ++ nextSeq = av.getAlignment().getSequenceAt(i); ++ ++ if (nextSeq == null) ++ { ++ continue; ++ } ++ ++ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq), ++ startRes, endRes, offset + ((i - startSeq) * av.charHeight)); ++ ++ if (av.isShowSequenceFeatures()) ++ { ++ fr.drawSequence(g, nextSeq, startRes, endRes, offset ++ + ((i - startSeq) * av.charHeight)); ++ } ++ ++ // / Highlight search Results once all sequences have been drawn ++ // //////////////////////////////////////////////////////// ++ if (searchResults != null) ++ { ++ int[] visibleResults = searchResults.getResults(nextSeq, startRes, ++ endRes); ++ if (visibleResults != null) ++ { ++ for (int r = 0; r < visibleResults.length; r += 2) ++ { ++ sr.drawHighlightedText(nextSeq, visibleResults[r], ++ visibleResults[r + 1], (visibleResults[r] - startRes) ++ * av.charWidth, offset ++ + ((i - startSeq) * av.charHeight)); ++ } ++ } ++ } ++ ++ if (av.cursorMode && cursorY == i && cursorX >= startRes ++ && cursorX <= endRes) ++ { ++ sr.drawCursor(nextSeq, cursorX, ++ (cursorX - startRes) * av.charWidth, offset ++ + ((i - startSeq) * av.charHeight)); ++ } ++ } ++ ++ if (av.getSelectionGroup() != null ++ || av.getAlignment().getGroups().size() > 0) ++ { ++ drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset); ++ } ++ ++ } ++ ++ void drawGroupsBoundaries(Graphics g, int startRes, int endRes, ++ int startSeq, int endSeq, int offset) ++ { ++ // ++ // /////////////////////////////////// ++ // Now outline any areas if necessary ++ // /////////////////////////////////// ++ SequenceGroup group = av.getSelectionGroup(); ++ ++ int sx = -1; ++ int sy = -1; ++ int ex = -1; ++ int groupIndex = -1; ++ ++ if ((group == null) && (av.getAlignment().getGroups().size() > 0)) ++ { ++ group = av.getAlignment().getGroups().get(0); ++ groupIndex = 0; ++ } ++ ++ if (group != null) ++ { ++ do ++ { ++ int oldY = -1; ++ int i = 0; ++ boolean inGroup = false; ++ int top = -1; ++ int bottom = -1; ++ int alHeight = av.getAlignment().getHeight() - 1; ++ ++ for (i = startSeq; i < endSeq; i++) ++ { ++ sx = (group.getStartRes() - startRes) * av.charWidth; ++ sy = offset + ((i - startSeq) * av.charHeight); ++ ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1; ++ ++ if (sx + ex < 0 || sx > imgWidth) ++ { ++ continue; ++ } ++ ++ if ((sx <= (endRes - startRes) * av.charWidth) ++ && group.getSequences(null).contains( ++ av.getAlignment().getSequenceAt(i))) ++ { ++ if ((bottom == -1) ++ && (i >= alHeight || !group.getSequences(null) ++ .contains( ++ av.getAlignment().getSequenceAt(i + 1)))) ++ { ++ bottom = sy + av.charHeight; ++ } ++ ++ if (!inGroup) ++ { ++ if (((top == -1) && (i == 0)) ++ || !group.getSequences(null).contains( ++ av.getAlignment().getSequenceAt(i - 1))) ++ { ++ top = sy; ++ } ++ ++ oldY = sy; ++ inGroup = true; ++ ++ if (group == av.getSelectionGroup()) ++ { ++ g.setColor(Color.red); ++ } ++ else ++ { ++ g.setColor(group.getOutlineColour()); ++ } ++ } ++ } ++ else ++ { ++ if (inGroup) ++ { ++ if (sx >= 0 && sx < imgWidth) ++ { ++ g.drawLine(sx, oldY, sx, sy); ++ } ++ ++ if (sx + ex < imgWidth) ++ { ++ g.drawLine(sx + ex, oldY, sx + ex, sy); ++ } ++ ++ if (sx < 0) ++ { ++ ex += sx; ++ sx = 0; ++ } ++ ++ if (sx + ex > imgWidth) ++ { ++ ex = imgWidth; ++ } ++ ++ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) ++ { ++ ex = (endRes - startRes + 1) * av.charWidth; ++ } ++ ++ if (top != -1) ++ { ++ g.drawLine(sx, top, sx + ex, top); ++ top = -1; ++ } ++ ++ if (bottom != -1) ++ { ++ g.drawLine(sx, bottom, sx + ex, bottom); ++ bottom = -1; ++ } ++ ++ inGroup = false; ++ } ++ } ++ } ++ ++ if (inGroup) ++ { ++ sy = offset + ((i - startSeq) * av.charHeight); ++ if (sx >= 0 && sx < imgWidth) ++ { ++ g.drawLine(sx, oldY, sx, sy); ++ } ++ ++ if (sx + ex < imgWidth) ++ { ++ g.drawLine(sx + ex, oldY, sx + ex, sy); ++ } ++ ++ if (sx < 0) ++ { ++ ex += sx; ++ sx = 0; ++ } ++ ++ if (sx + ex > imgWidth) ++ { ++ ex = imgWidth; ++ } ++ else if (sx + ex >= (endRes - startRes + 1) * av.charWidth) ++ { ++ ex = (endRes - startRes + 1) * av.charWidth; ++ } ++ ++ if (top != -1) ++ { ++ g.drawLine(sx, top, sx + ex, top); ++ top = -1; ++ } ++ ++ if (bottom != -1) ++ { ++ g.drawLine(sx, bottom - 1, sx + ex, bottom - 1); ++ bottom = -1; ++ } ++ ++ inGroup = false; ++ } ++ ++ groupIndex++; ++ ++ if (groupIndex >= av.getAlignment().getGroups().size()) ++ { ++ break; ++ } ++ ++ group = av.getAlignment().getGroups() ++ .get(groupIndex); ++ } while (groupIndex < av.getAlignment().getGroups().size()); ++ ++ } ++ } ++ ++ public void highlightSearchResults(SearchResults results) ++ { ++ searchResults = results; ++ ++ repaint(); ++ } ++ ++} diff --cc src/jalview/datamodel/ColumnSelection.java index f1c6cc4,93e03d1..6acca32 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@@ -21,8 -21,10 +21,11 @@@ package jalview.datamodel; import jalview.util.ShiftList; + import jalview.viewmodel.annotationfilter.AnnotationFilterParameter; + import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField; import java.util.ArrayList; ++import java.util.Arrays; import java.util.Enumeration; import java.util.List; import java.util.Vector; @@@ -477,16 -479,16 +480,13 @@@ public class ColumnSelectio } /** -- * This Method is used to return all the HiddenColumn regions less than the -- * given index. -- * -- * @param end -- * int -- * @return Vector ++ * This Method is used to return all the HiddenColumn regions ++ * @return empty list or List of hidden column intervals */ - public Vector getHiddenColumns() + public List getHiddenColumns() { -- return hiddenColumns; ++ return hiddenColumns == null ? Arrays.asList(new int[] ++ {}) : hiddenColumns; } /** @@@ -1266,36 -1268,88 +1266,130 @@@ } } + /** + * + * @return true if there are columns marked + */ + public boolean hasSelectedColumns() + { + return (selected != null && selected.size() > 0); + } + + /** + * + * @return true if there are columns hidden + */ + public boolean hasHiddenColumns() + { + return hiddenColumns != null && hiddenColumns.size() > 0; + } ++ ++ /** ++ * ++ * @return true if there are more than one set of columns hidden ++ */ ++ public boolean hasManyHiddenColumns() ++ { ++ return hiddenColumns != null && hiddenColumns.size() > 1; ++ } + + /** + * mark the columns corresponding to gap characters as hidden in the column + * selection + * + * @param sr + */ + public void hideInsertionsFor(SequenceI sr) + { + List inserts = sr.getInsertions(); + for (int[] r : inserts) + { + hideColumns(r[0], r[1]); + } + } ++ + public boolean filterAnnotations(Annotation[] annotations, + AnnotationFilterParameter filterParams) + { + this.revealAllHiddenColumns(); + this.clear(); + int count = 0; + do + { + if (annotations[count] != null) + { + + boolean itemMatched = false; + + if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD + && annotations[count].value >= filterParams + .getThresholdValue()) + { + itemMatched = true; + } + if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD + && annotations[count].value <= filterParams + .getThresholdValue()) + { + itemMatched = true; + } + + if (filterParams.isFilterAlphaHelix() + && annotations[count].secondaryStructure == 'H') + { + itemMatched = true; + } + + if (filterParams.isFilterBetaSheet() + && annotations[count].secondaryStructure == 'E') + { + itemMatched = true; + } + + if (filterParams.isFilterTurn() + && annotations[count].secondaryStructure == 'S') + { + itemMatched = true; + } + + String regexSearchString = filterParams.getRegexString(); + if (regexSearchString != null + && !filterParams.getRegexSearchFields().isEmpty()) + { + List fields = filterParams + .getRegexSearchFields(); + try + { + if (fields.contains(SearchableAnnotationField.DISPLAY_STRING) + && annotations[count].displayCharacter + .matches(regexSearchString)) + { + itemMatched = true; + } + } catch (java.util.regex.PatternSyntaxException pse) + { + if (annotations[count].displayCharacter + .equals(regexSearchString)) + { + itemMatched = true; + } + } + if (fields.contains(SearchableAnnotationField.DESCRIPTION) + && annotations[count].description != null + && annotations[count].description + .matches(regexSearchString)) + { + itemMatched = true; + } + } + + if (itemMatched) + { + this.addElement(count); + } + } + count++; + } while (count < annotations.length); + return false; + } }