X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreeCanvas.java;h=45def89ebb7c1ffb82707cc6b3b1a6569b5313e7;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=0e513f77008dee2bc73b146c90279b8138a4c21c;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 0e513f7..45def89 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -21,7 +21,7 @@ package jalview.gui; import jalview.analysis.Conservation; -import jalview.analysis.NJTree; +import jalview.analysis.TreeModel; import jalview.api.AlignViewportI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; @@ -53,6 +53,7 @@ import java.awt.print.PrinterException; import java.awt.print.PrinterJob; import java.util.Enumeration; import java.util.Hashtable; +import java.util.List; import java.util.Vector; import javax.swing.JColorChooser; @@ -73,15 +74,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, /** DOCUMENT ME!! */ public static final String PLACEHOLDER = " * "; - NJTree tree; + TreeModel tree; JScrollPane scrollPane; TreePanel tp; - AlignViewport av; + private AlignViewport av; - AlignmentPanel ap; + private AlignmentPanel ap; Font font; @@ -99,7 +100,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, int offy; - float threshold; + private float threshold; String longestName; @@ -129,7 +130,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { this.tp = tp; this.av = ap.av; - this.ap = ap; + this.setAssociatedPanel(ap); font = av.getFont(); scrollPane = scroller; addMouseListener(this); @@ -168,7 +169,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * @param tree * DOCUMENT ME! */ - public void setTree(NJTree tree) + public void setTree(TreeModel tree) { this.tree = tree; tree.findHeight(tree.getTopNode()); @@ -207,7 +208,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * @param chunk * DOCUMENT ME! - * @param scale + * @param wscale * DOCUMENT ME! * @param width * DOCUMENT ME! @@ -217,7 +218,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! */ public void drawNode(Graphics g, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + double wscale, int width, int offx, int offy) { if (node == null) { @@ -227,11 +228,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { // Drawing leaf node - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; + int xstart = (int) ((height - dist) * wscale) + offx; + int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -278,8 +279,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && node.isPlaceholder()) ? (PLACEHOLDER + node - .getName()) : node.getName(); + String name = (markPlaceholders && node.isPlaceholder()) + ? (PLACEHOLDER + node.getName()) + : node.getName(); int charWidth = fm.stringWidth(name) + 3; int charHeight = font.getSize(); @@ -306,16 +308,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - drawNode(g, (SequenceNode) node.left(), chunk, scale, width, offx, + drawNode(g, (SequenceNode) node.left(), chunk, wscale, width, offx, offy); - drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx, + drawNode(g, (SequenceNode) node.right(), chunk, wscale, width, offx, offy); - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; + int xstart = (int) ((height - dist) * wscale) + offx; + int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; g.setColor(node.color.darker()); @@ -331,16 +333,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g.fillRect(xend - 2, ypos - 2, 4, 4); } - int ystart = (int) (((SequenceNode) node.left()).ycount * chunk) - + offy; - int yend = (int) (((SequenceNode) node.right()).ycount * chunk) + int ystart = (node.left() == null ? 0 + : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy; + int yend = (node.right() == null ? 0 + : (int) (((SequenceNode) node.right()).ycount * chunk)) + offy; Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5); nodeHash.put(node, pos); - g.drawLine((int) (height * scale) + offx, ystart, - (int) (height * scale) + offx, yend); + g.drawLine((int) (height * wscale) + offx, ystart, + (int) (height * wscale) + offx, yend); String nodeLabel = ""; @@ -422,8 +425,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, SequenceNode top = tree.getTopNode(); - float wscale = (float) ((width * .8) - (offx * 2)) - / tree.getMaxHeight(); + double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight(); if (top.count == 0) { @@ -445,7 +447,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! * @param chunk * DOCUMENT ME! - * @param scale + * @param wscale * DOCUMENT ME! * @param width * DOCUMENT ME! @@ -455,7 +457,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, * DOCUMENT ME! */ public void pickNode(Rectangle pickBox, SequenceNode node, float chunk, - float scale, int width, int offx, int offy) + double wscale, int width, int offx, int offy) { if (node == null) { @@ -464,11 +466,11 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if ((node.left() == null) && (node.right() == null)) { - float height = node.height; - float dist = node.dist; + double height = node.height; + double dist = node.dist; - int xstart = (int) ((height - dist) * scale) + offx; - int xend = (int) (height * scale) + offx; + int xstart = (int) ((height - dist) * wscale) + offx; + int xend = (int) (height * wscale) + offx; int ypos = (int) (node.ycount * chunk) + offy; @@ -488,9 +490,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width, + pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width, offx, offy); - pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width, + pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width, offx, offy); } } @@ -549,7 +551,16 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, public void run() { PrinterJob printJob = PrinterJob.getPrinterJob(); - PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + PageFormat defaultPage = printJob.defaultPage(); + PageFormat pf = printJob.pageDialog(defaultPage); + + if (defaultPage == pf) + { + /* + * user cancelled + */ + return; + } printJob.setPrintable(this, pf); @@ -643,8 +654,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (tree == null) { - g.drawString(MessageManager.getString("label.calculating_tree") - + "....", 20, getHeight() / 2); + g.drawString( + MessageManager.getString("label.calculating_tree") + "....", + 20, getHeight() / 2); } else { @@ -655,9 +667,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, repaint(); } - if (fitToWindow - || (!fitToWindow && (scrollPane.getHeight() > ((fm - .getHeight() * nameHash.size()) + offy)))) + if (fitToWindow || (!fitToWindow && (scrollPane + .getHeight() > ((fm.getHeight() * nameHash.size()) + offy)))) { draw(g, scrollPane.getWidth(), scrollPane.getHeight()); setPreferredSize(null); @@ -715,7 +726,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, labelLength = fm.stringWidth(longestName) + 20; // 20 allows for scrollbar - float wscale = (width - labelLength - (offx * 2)) / tree.getMaxHeight(); + double wscale = (width - labelLength - (offx * 2)) + / tree.getMaxHeight(); SequenceNode top = tree.getTopNode(); @@ -740,7 +752,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, g2.setColor(Color.gray); } - int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + offx); + int x = (int) ((threshold * (getWidth() - labelLength - (2 * offx))) + + offx); g2.drawLine(x, 0, x, getHeight()); } @@ -834,7 +847,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (col != null) { setColor(highlightNode, col); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); } } @@ -849,8 +862,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceNode) { highlightNode = (SequenceNode) ob; - this.setToolTipText("" - + MessageManager.getString("label.highlightnode")); + this.setToolTipText( + "" + MessageManager.getString("label.highlightnode")); repaint(); } @@ -915,7 +928,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (ob instanceof SequenceI) { treeSelectionChanged((Sequence) ob); - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); av.sendSelection(); return; @@ -928,8 +941,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, threshold = (float) (x - offx) / (float) (getWidth() - labelLength - (2 * offx)); - tree.getGroups().removeAllElements(); - tree.groupNodes(tree.getTopNode(), threshold); + List groups = tree.groupNodes(threshold); setColor(tree.getTopNode(), Color.black); AlignmentPanel[] aps = getAssociatedPanels(); @@ -949,28 +961,36 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, aps[a].av.getCodingComplement().clearSequenceColours(); } } - colourGroups(); + colourGroups(groups); + + /* + * clear partition (don't show vertical line) if + * it is to the right of all nodes + */ + if (groups.isEmpty()) + { + threshold = 0f; + } } - PaintRefresher.Refresh(tp, ap.av.getSequenceSetId()); + PaintRefresher.Refresh(tp, getAssociatedPanel().av.getSequenceSetId()); repaint(); } } - void colourGroups() + void colourGroups(List groups) { AlignmentPanel[] aps = getAssociatedPanels(); - for (int i = 0; i < tree.getGroups().size(); i++) + for (int i = 0; i < groups.size(); i++) { Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); - setColor(tree.getGroups().elementAt(i), col.brighter()); + setColor(groups.get(i), col.brighter()); - Vector l = tree.findLeaves(tree.getGroups() - .elementAt(i)); + Vector l = tree.findLeaves(groups.get(i)); - Vector sequences = new Vector(); + Vector sequences = new Vector<>(); for (int j = 0; j < l.size(); j++) { @@ -997,17 +1017,20 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty + cs = ColourSchemeProperty.getColourScheme(sg, ColourSchemeProperty .getColourName(av.getGlobalColourScheme())); } // cs is null if shading is an annotationColourGradient - if (cs != null) - { - cs.setThreshold(av.getGlobalColourScheme().getThreshold(), - av.isIgnoreGapsConsensus()); - } + // if (cs != null) + // { + // cs.setThreshold(av.getViewportColourScheme().getThreshold(), + // av.isIgnoreGapsConsensus()); + // } } - sg.cs = cs; + sg.setColourScheme(cs); + sg.getGroupColourScheme().setThreshold( + av.getResidueShading().getThreshold(), + av.isIgnoreGapsConsensus()); // sg.recalcConservation(); sg.setName("JTreeGroup:" + sg.hashCode()); sg.setIdColour(col); @@ -1015,10 +1038,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, for (int a = 0; a < aps.length; a++) { if (aps[a].av.getGlobalColourScheme() != null - && aps[a].av.getGlobalColourScheme().conservationApplied()) + && aps[a].av.getResidueShading().conservationApplied()) { - Conservation c = new Conservation("Group", 3, - sg.getSequences(null), sg.getStartRes(), sg.getEndRes()); + Conservation c = new Conservation("Group", sg.getSequences(null), + sg.getStartRes(), sg.getEndRes()); c.calculate(); c.verdict(false, aps[a].av.getConsPercGaps()); sg.cs.setConservation(c); @@ -1104,7 +1127,37 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } else { - return new AlignmentPanel[] { ap }; + return new AlignmentPanel[] { getAssociatedPanel() }; } } + + public AlignmentPanel getAssociatedPanel() + { + return ap; + } + + public void setAssociatedPanel(AlignmentPanel ap) + { + this.ap = ap; + } + + public AlignViewport getViewport() + { + return av; + } + + public void setViewport(AlignViewport av) + { + this.av = av; + } + + public float getThreshold() + { + return threshold; + } + + public void setThreshold(float threshold) + { + this.threshold = threshold; + } }