X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPCAPanel.java;h=ea4f44e2f7bc3ab40aee3dd63439053f70fbba44;hb=0b23947e2cdcd704d3f313b23ba271e43d097344;hp=8685b3eb74d5af31a9eef3c7e48319b5f174dc75;hpb=48b0a1554f4885581d99dac216a83780ceceb41a;p=jalview.git diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 8685b3e..ea4f44e 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -28,7 +28,8 @@ import java.awt.*; import java.awt.event.*; import java.util.*; -import javax.swing.JOptionPane; +import javax.swing.*; +import java.awt.print.*; /** @@ -43,7 +44,8 @@ public class PCAPanel extends GPCAPanel implements Runnable int top; RotatableCanvas rc; AlignViewport av; - SequenceI [] seqs; + AlignmentView seqstrings; + SequenceI [] seqs; /** * Creates a new PCAPanel object. @@ -55,33 +57,63 @@ public class PCAPanel extends GPCAPanel implements Runnable { this.av = av; - if ((av.getSelectionGroup() != null) && - (av.getSelectionGroup().getSize() > 3)) - { - seqs = new Sequence[av.getSelectionGroup().getSize()]; + boolean sameLength = true; - for (int i = 0; i < av.getSelectionGroup().getSize(); i++) - { - seqs[i] = av.getSelectionGroup().getSequenceAt(i); - } + seqstrings = av.getAlignmentView(av.getSelectionGroup()!=null); + if(av.getSelectionGroup()==null) + { + seqs = av.alignment.getSequencesArray(); } else { - seqs = new Sequence[av.getAlignment().getHeight()]; + seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment); + } + SeqCigar sq[]=seqstrings.getSequences(); + int length = sq[0].getWidth(); - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - seqs[i] = av.getAlignment().getSequenceAt(i); - } + for (int i = 0; i < seqs.length; i++) + { + if (sq[i].getWidth() != length) + { + sameLength = false; + break; + } + } + + if (!sameLength) + { + JOptionPane.showMessageDialog(Desktop.desktop, + "The sequences must be aligned before calculating PCA.\n" + + "Try using the Pad function in the edit menu,\n" + + "or one of the multiple sequence alignment web services.", + "Sequences not aligned", + JOptionPane.WARNING_MESSAGE); + + return; } + Desktop.addInternalFrame(this, "Principal component analysis", + 400, 400); + + rc = new RotatableCanvas(av); - add(rc, BorderLayout.CENTER); + this.getContentPane().add(rc, BorderLayout.CENTER); Thread worker = new Thread(this); worker.start(); } + public void bgcolour_actionPerformed(ActionEvent e) + { + Color col = JColorChooser.showDialog(this, "Select Background Colour", + rc.bgColour); + + if(col!=null) + rc.bgColour = col; + rc.repaint(); + } + + /** @@ -90,7 +122,7 @@ public class PCAPanel extends GPCAPanel implements Runnable public void run() { try{ - pca = new PCA(seqs); + pca = new PCA(seqstrings.getSequenceStrings(' ')); pca.run(); // Now find the component coordinates @@ -129,7 +161,6 @@ public class PCAPanel extends GPCAPanel implements Runnable rc.setPoints(points, pca.getM().rows); rc.repaint(); - seqs = null; } catch(OutOfMemoryError er) { JOptionPane.showInternalMessageDialog(Desktop.desktop, @@ -201,4 +232,182 @@ public class PCAPanel extends GPCAPanel implements Runnable { doDimensionChange(); } -} + + + public void outputValues_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + Desktop.addInternalFrame(cap, "PCA details", 500, + 500); + + cap.setText(pca.getDetails()); + } + + public void showLabels_actionPerformed(ActionEvent e) + { + rc.showLabels(showLabels.getState()); + } + + public void print_actionPerformed(ActionEvent e) + { + PCAPrinter printer = new PCAPrinter(); + printer.start(); + } + + public void originalSeqData_actionPerformed(ActionEvent e) + { + // this was cut'n'pasted from the equivalent TreePanel method - we should make this an abstract function of all jalview analysis windows + if (seqstrings==null) + { + jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action."); + return; + } + // decide if av alignment is sufficiently different to original data to warrant a new window to be created + // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs) + // or create a selection box around columns in alignment view + // test Alignment(SeqCigar[]) + Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av. + getGapCharacter()); + + + if (alAndColsel != null && alAndColsel[0]!=null) + { + // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]); + + Alignment al = new Alignment((SequenceI[]) alAndColsel[0]); + Alignment dataset = av.getAlignment().getDataset(); + if (dataset != null) + { + al.setDataset(dataset); + } + + if (true) + { + // make a new frame! + AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1], + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT +); + + //>>>This is a fix for the moment, until a better solution is found!!<<< + // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer()); + + // af.addSortByOrderMenuItem(ServiceName + " Ordering", + // msaorder); + + Desktop.addInternalFrame(af, "Original Data for " + this.title, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + } + /* CutAndPasteTransfer cap = new CutAndPasteTransfer(); + for (int i = 0; i < seqs.length; i++) + { + cap.appendText(new jalview.util.Format("%-" + 15 + "s").form( + seqs[i].getName())); + cap.appendText(" " + seqstrings[i] + "\n"); + + } + + Desktop.addInternalFrame(cap, "Original Data", + 400, 400); + */ + } + + + + class PCAPrinter extends Thread implements Printable + { + public void run() + { + PrinterJob printJob = PrinterJob.getPrinterJob(); + PageFormat pf = printJob.pageDialog(printJob.defaultPage()); + + printJob.setPrintable(this, pf); + + if (printJob.printDialog()) + { + try + { + printJob.print(); + } + catch (Exception PrintException) + { + PrintException.printStackTrace(); + } + } + } + + public int print(Graphics pg, PageFormat pf, int pi) + throws PrinterException + { + pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY()); + + rc.drawBackground(pg, rc.bgColour); + rc.drawScene(pg); + if (rc.drawAxes == true) + { + rc.drawAxes(pg); + } + + if (pi == 0) + return Printable.PAGE_EXISTS; + else + return Printable.NO_SUCH_PAGE; + } + } + + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void eps_actionPerformed(ActionEvent e) + { + makePCAImage(jalview.util.ImageMaker.EPS); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void png_actionPerformed(ActionEvent e) + { + makePCAImage(jalview.util.ImageMaker.PNG); + } + + void makePCAImage(int type) + { + int width = rc.getWidth(); + int height = rc.getHeight(); + + jalview.util.ImageMaker im; + + if(type == jalview.util.ImageMaker.PNG) + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.PNG, + "Make PNG image from PCA", + width, height, + null, null); + else + im = new jalview.util.ImageMaker(this, + jalview.util.ImageMaker.EPS, + "Make EPS file from PCA", + width, height, + null, this.getTitle()); + + if(im.getGraphics()!=null) + { + rc.drawBackground(im.getGraphics(), Color.black); + rc.drawScene(im.getGraphics()); + if (rc.drawAxes == true) + { + rc.drawAxes(im.getGraphics()); + } + im.writeImage(); + } + } + }