X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=d7a8f001c5f34599ebaf0dfbb06d22e9d1c0c20e;hp=d35a0f40a19b1071f6d998f75f89b17c545f07b6;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=6abefac67f193512eb944881446b206f891be06e diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index d35a0f4..d7a8f00 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,394 +1,513 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import jalview.datamodel.*; - -import java.awt.*; -import java.awt.image.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class IdCanvas extends JPanel -{ - protected AlignViewport av; - protected boolean showScores = true; - protected int maxIdLength = -1; - protected String maxIdStr = null; - BufferedImage image; - Graphics2D gg; - int imgHeight = 0; - boolean fastPaint = false; - java.util.Vector searchResults; - - /** - * Creates a new IdCanvas object. - * - * @param av DOCUMENT ME! - */ - public IdCanvas(AlignViewport av) - { - setLayout(new BorderLayout()); - this.av = av; - PaintRefresher.Register(this, av.alignment); - } - - /** - * DOCUMENT ME! - * - * @param gg DOCUMENT ME! - * @param s DOCUMENT ME! - * @param i DOCUMENT ME! - * @param starty DOCUMENT ME! - * @param ypos DOCUMENT ME! - */ - public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, int ypos) - { - int charHeight = av.charHeight; - - if ((searchResults != null) && searchResults.contains(s)) - { - gg.setColor(Color.black); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), - charHeight); - gg.setColor(Color.white); - } - else if ((av.getSelectionGroup() != null) && - av.getSelectionGroup().getSequences(false).contains(s)) - { - gg.setColor(Color.lightGray); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), - charHeight); - gg.setColor(Color.white); - } - else - { - gg.setColor(s.getColor()); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), - charHeight); - gg.setColor(Color.black); - } - - - gg.drawString( s.getDisplayId(av.getShowJVSuffix()), - 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); - - if (av.hasHiddenRows && av.showHiddenMarkers) - drawMarker(i, starty, ypos); - - - } - - /** - * DOCUMENT ME! - * - * @param vertical DOCUMENT ME! - */ - public void fastPaint(int vertical) - { - if (gg == null) - { - repaint(); - - return; - } - - gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight); - - int ss = av.startSeq; - int es = av.endSeq; - int transY = 0; - - 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(0, transY); - - drawIds(ss, es); - - gg.translate(0, -transY); - - fastPaint = true; - repaint(); - } - - /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! - */ - public void paintComponent(Graphics g) - { - g.setColor(Color.white); - g.fillRect(0, 0, getWidth(), getHeight()); - - if (fastPaint) - { - fastPaint = false; - g.drawImage(image, 0, 0, this); - - return; - } - - int oldHeight = imgHeight; - - imgHeight = getHeight(); - imgHeight -= (imgHeight % av.charHeight); - - if (imgHeight < 1) - { - return; - } - - if(oldHeight!=imgHeight) - { - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); - gg = (Graphics2D) image.getGraphics(); - } - - //Fill in the background - gg.setColor(Color.white); - gg.fillRect(0, 0, getWidth(), imgHeight); - - drawIds(av.getStartSeq(), av.endSeq); - - g.drawImage(image, 0, 0, this); - } - - /** - * DOCUMENT ME! - * - * @param starty DOCUMENT ME! - * @param endy DOCUMENT ME! - */ - void drawIds(int starty, int endy) - { - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); - - gg.setFont(italic); - - if (av.antiAlias) - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); - - Color currentColor = Color.white; - Color currentTextColor = Color.black; - - 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) - { - AnnotationPanel ap = new AnnotationPanel(av); - annotationHeight = ap.adjustPanelHeight(); - labels = new AnnotationLabels(av); - } - - int hgap = av.charHeight; - if (av.scaleAboveWrapped) - hgap += av.charHeight; - - int cHeight = alheight * av.charHeight - + hgap - + annotationHeight; - - int rowSize = av.getEndRes() - av.getStartRes(); - - - // Draw the rest of the panels - for (int ypos = hgap, row = av.startRes; - (ypos <= getHeight()) && (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); - } - - if(labels!=null) - { - gg.translate(0, ypos+(alheight * av.charHeight)); - labels.drawComponent(gg, getWidth()); - gg.translate(0, -ypos-(alheight * av.charHeight)); - } - - - } - } - else - { - //Now draw the id strings - - //Now draw the id strings - for (int i = starty; i < endy; i++) - { - if (av.hasHiddenRows) - { - setHiddenFont(i); - } - - // Selected sequence colours - if ( (searchResults != null) && - searchResults.contains(av.alignment.getSequenceAt(i))) - { - currentColor = Color.black; - currentTextColor = Color.white; - } - else if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().getSequences(false).contains( - av.alignment.getSequenceAt(i))) - { - currentColor = Color.lightGray; - currentTextColor = Color.black; - } - else - { - currentColor = av.alignment.getSequenceAt(i).getColor(); - currentTextColor = Color.black; - } - - gg.setColor(currentColor); - - gg.fillRect(0, (i - starty) * av.charHeight, getWidth(), - av.charHeight); - - gg.setColor(currentTextColor); - - String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix()); - - gg.drawString(string, 0, - (((i - starty) * av.charHeight) + av.charHeight) - - (av.charHeight / 5)); - - if(av.hasHiddenRows && av.showHiddenMarkers) - drawMarker(i, starty, 0); - - } - - } - } - - 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); - - boolean below = (hiddenIndex > lastIndex + 1); - boolean above = (nextIndex>hiddenIndex+1); - - gg.setColor(Color.blue); - if(below) - { - gg.fillPolygon(new int[] - {getWidth()- av.charHeight, - getWidth()- av.charHeight, - getWidth()}, - 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[] - {getWidth()- av.charHeight, - getWidth()- av.charHeight, - getWidth() }, - 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) - { - Font italic = new Font(av.getFont().getName(), Font.ITALIC, - av.getFont().getSize()); - Font bold = new Font(av.getFont().getName(), Font.BOLD, - av.getFont().getSize()); - - if (av.alignment.getSequenceAt(i).getHiddenSequences() != null) - gg.setFont(bold); - else - gg.setFont(italic); - } - - /** - * DOCUMENT ME! - * - * @param found DOCUMENT ME! - */ - public void setHighlighted(java.util.Vector found) - { - searchResults = found; - repaint(); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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.gui; + +import jalview.datamodel.SequenceI; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.RenderingHints; +import java.awt.image.BufferedImage; +import java.util.List; + +import javax.swing.JPanel; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class IdCanvas extends JPanel +{ + protected AlignViewport av; + + protected boolean showScores = true; + + protected int maxIdLength = -1; + + protected String maxIdStr = null; + + BufferedImage image; + + Graphics2D gg; + + int imgHeight = 0; + + boolean fastPaint = false; + + List searchResults; + + FontMetrics fm; + + AnnotationLabels labels = null; + + AnnotationPanel ap; + + private Font idfont; + + /** + * Creates a new IdCanvas object. + * + * @param av + * DOCUMENT ME! + */ + public IdCanvas(AlignViewport av) + { + setLayout(new BorderLayout()); + this.av = av; + PaintRefresher.Register(this, av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param gg + * DOCUMENT ME! + * @param hiddenRows + * true - check and display hidden row marker if need be + * @param s + * DOCUMENT ME! + * @param i + * DOCUMENT ME! + * @param starty + * DOCUMENT ME! + * @param ypos + * DOCUMENT ME! + */ + public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s, + int i, int starty, int ypos) + { + int xPos = 0; + int panelWidth = getWidth(); + int charHeight = av.getCharHeight(); + + if ((searchResults != null) && searchResults.contains(s)) + { + gg.setColor(Color.black); + gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + charHeight); + gg.setColor(Color.white); + } + else if ((av.getSelectionGroup() != null) + && av.getSelectionGroup().getSequences(null).contains(s)) + { + gg.setColor(Color.lightGray); + gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + charHeight); + gg.setColor(Color.white); + } + else + { + gg.setColor(av.getSequenceColour(s)); + gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + charHeight); + gg.setColor(Color.black); + } + + if (av.isRightAlignIds()) + { + xPos = panelWidth + - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; + } + + gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, + (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); + + if (hiddenRows) + { + drawMarker(i, starty, ypos); + } + + } + + /** + * DOCUMENT ME! + * + * @param vertical + * DOCUMENT ME! + */ + public void fastPaint(int vertical) + { + if (gg == null) + { + repaint(); + + return; + } + + gg.copyArea(0, 0, getWidth(), imgHeight, 0, + -vertical * av.getCharHeight()); + + int ss = av.startSeq; + int es = av.endSeq; + int transY = 0; + + 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.getCharHeight()); + } + } + else if (vertical < 0) + { + es = ss - vertical; + + if (es > av.endSeq) + { + es = av.endSeq; + } + } + + gg.translate(0, transY); + + drawIds(ss, es); + + gg.translate(0, -transY); + + fastPaint = true; + repaint(); + } + + /** + * DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + */ + public void paintComponent(Graphics g) + { + g.setColor(Color.white); + g.fillRect(0, 0, getWidth(), getHeight()); + + if (fastPaint) + { + fastPaint = false; + g.drawImage(image, 0, 0, this); + + return; + } + + int oldHeight = imgHeight; + + imgHeight = getHeight(); + imgHeight -= (imgHeight % av.getCharHeight()); + + if (imgHeight < 1) + { + return; + } + + if (oldHeight != imgHeight || image.getWidth(this) != getWidth()) + { + image = new BufferedImage(getWidth(), imgHeight, + BufferedImage.TYPE_INT_RGB); + } + + gg = (Graphics2D) image.getGraphics(); + + // Fill in the background + gg.setColor(Color.white); + gg.fillRect(0, 0, getWidth(), imgHeight); + + drawIds(av.getStartSeq(), av.endSeq); + + g.drawImage(image, 0, 0, this); + } + + /** + * DOCUMENT ME! + * + * @param starty + * DOCUMENT ME! + * @param endy + * DOCUMENT ME! + */ + void drawIds(int starty, int endy) + { + if (av.isSeqNameItalics()) + { + setIdfont(new Font(av.getFont().getName(), Font.ITALIC, av.getFont() + .getSize())); + } + else + { + setIdfont(av.getFont()); + } + + gg.setFont(getIdfont()); + fm = gg.getFontMetrics(); + + if (av.antiAlias) + { + gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + RenderingHints.VALUE_ANTIALIAS_ON); + } + + Color currentColor = Color.white; + Color currentTextColor = Color.black; + + final boolean doHiddenCheck = av.isDisplayReferenceSeq() + || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows(); + + if (av.getWrapAlignment()) + { + int maxwidth = av.getAlignment().getWidth(); + int alheight = av.getAlignment().getHeight(); + + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + } + + int annotationHeight = 0; + + if (av.isShowAnnotation()) + { + if (ap == null) + { + ap = new AnnotationPanel(av); + } + + annotationHeight = ap.adjustPanelHeight(); + if (labels == null) + { + labels = new AnnotationLabels(av); + } + } + + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) + { + hgap += av.getCharHeight(); + } + + int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight; + + int rowSize = av.getEndRes() - av.getStartRes(); + + // Draw the rest of the panels + for (int ypos = hgap, row = av.startRes; (ypos <= getHeight()) + && (row < maxwidth); ypos += cHeight, row += rowSize) + { + for (int i = starty; i < alheight; i++) + { + SequenceI s = av.getAlignment().getSequenceAt(i); + if (doHiddenCheck) + { + setHiddenFont(s); + } + else + { + gg.setFont(getIdfont()); + } + + drawIdString(gg, hiddenRows, s, i, 0, ypos); + } + + if (labels != null && av.isShowAnnotation()) + { + gg.translate(0, ypos + (alheight * av.getCharHeight())); + labels.drawComponent(gg, getWidth()); + gg.translate(0, -ypos - (alheight * av.getCharHeight())); + } + } + } + else + { + // No need to hang on to labels if we're not wrapped + labels = null; + + // Now draw the id strings + int panelWidth = getWidth(); + int xPos = 0; + + SequenceI sequence; + // Now draw the id strings + for (int i = starty; i < endy; i++) + { + sequence = av.getAlignment().getSequenceAt(i); + + if (sequence == null) + { + continue; + } + + if (doHiddenCheck) + { + setHiddenFont(sequence); + } + + // Selected sequence colours + if ((searchResults != null) && searchResults.contains(sequence)) + { + currentColor = Color.black; + currentTextColor = Color.white; + } + else if ((av.getSelectionGroup() != null) + && av.getSelectionGroup().getSequences(null) + .contains(sequence)) + { + currentColor = Color.lightGray; + currentTextColor = Color.black; + } + else + { + currentColor = av.getSequenceColour(sequence); + currentTextColor = Color.black; + } + + gg.setColor(currentColor); + + gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(), + av.getCharHeight()); + + gg.setColor(currentTextColor); + + String string = sequence.getDisplayId(av.getShowJVSuffix()); + + if (av.isRightAlignIds()) + { + xPos = panelWidth - fm.stringWidth(string) - 4; + } + + gg.drawString(string, xPos, + (((i - starty) * av.getCharHeight()) + av.getCharHeight()) + - (av.getCharHeight() / 5)); + + if (hiddenRows) + { + drawMarker(i, starty, 0); + } + + } + + } + } + + void drawMarker(int i, int starty, int yoffset) + { + + SequenceI[] hseqs = av.getAlignment().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; + + for (int j = 0; j < hSize; j++) + { + if (hseqs[j] != null) + { + if (j - 1 < hiddenIndex) + { + hiddenIndex++; + } + if (j - 1 < lastIndex) + { + lastIndex++; + } + if (j - 1 < nextIndex) + { + nextIndex++; + } + } + } + + boolean below = (hiddenIndex > lastIndex + 1); + boolean above = (nextIndex > hiddenIndex + 1); + + gg.setColor(Color.blue); + if (below) + { + gg.fillPolygon( + new int[] { getWidth() - av.getCharHeight(), + getWidth() - av.getCharHeight(), getWidth() }, + new int[] { + (i - starty) * av.getCharHeight() + yoffset, + (i - starty) * av.getCharHeight() + yoffset + + av.getCharHeight() / 4, + (i - starty) * av.getCharHeight() + yoffset }, 3); + } + if (above) + { + gg.fillPolygon( + new int[] { getWidth() - av.getCharHeight(), + getWidth() - av.getCharHeight(), getWidth() }, + new int[] { + (i - starty + 1) * av.getCharHeight() + yoffset, + (i - starty + 1) * av.getCharHeight() + yoffset + - av.getCharHeight() / 4, + (i - starty + 1) * av.getCharHeight() + yoffset }, 3); + + } + } + + void setHiddenFont(SequenceI seq) + { + Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont() + .getSize()); + + if (av.isHiddenRepSequence(seq)) + { + gg.setFont(bold); + } + else + { + gg.setFont(getIdfont()); + } + } + + /** + * DOCUMENT ME! + * + * @param list + * DOCUMENT ME! + */ + public void setHighlighted(List list) + { + searchResults = list; + repaint(); + } + + public Font getIdfont() + { + return idfont; + } + + public void setIdfont(Font idfont) + { + this.idfont = idfont; + } +}