From 8c2ee75d86492f03e4c01404855f9ad2dd305719 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 8 Sep 2005 16:04:11 +0000 Subject: [PATCH] Init PCA in thread --- src/jalview/appletgui/PCAPanel.java | 108 ++++++++++++++-------------- src/jalview/appletgui/RotatableCanvas.java | 55 ++++++++------ src/jalview/gui/PCAPanel.java | 95 ++++++++++++------------ src/jalview/gui/RotatableCanvas.java | 54 ++++++-------- 4 files changed, 161 insertions(+), 151 deletions(-) diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java index 1dd05e0..f470ffc 100755 --- a/src/jalview/appletgui/PCAPanel.java +++ b/src/jalview/appletgui/PCAPanel.java @@ -35,11 +35,8 @@ public class PCAPanel int top; RotatableCanvas rc; AlignViewport av; + SequenceI [] seqs; - public void run() - { - // do stuff - } public PCAPanel(AlignViewport av, SequenceI[] s) { @@ -47,65 +44,72 @@ public class PCAPanel this.av = av; if (av.getSelectionGroup().getSize() > 3) { - s = new Sequence[av.getSelectionGroup().getSize()]; + seqs = new Sequence[av.getSelectionGroup().getSize()]; for (int i = 0; i < s.length; i++) { - s[i] = av.getSelectionGroup().getSequenceAt(i); + seqs[i] = av.getSelectionGroup().getSequenceAt(i); } } - if (s == null) + if (seqs == null) { - s = new Sequence[av.getAlignment().getHeight()]; + seqs = new Sequence[av.getAlignment().getHeight()]; for (int i = 0; i < av.getAlignment().getHeight(); i++) { - s[i] = av.getAlignment().getSequenceAt(i); - } - } - -//////////////////////This part was done in PCATHread originally. Is it too slow??? - pca = new PCA(s); - pca.run(); - - // Now find the component coordinates - int ii = 0; - while (ii < s.length && s[ii] != null) - { - ii++; - } - - double[][] comps = new double[ii][ii]; - - for (int i = 0; i < ii; i++) - { - if (pca.getEigenvalue(i) > 1e-4) - { - comps[i] = pca.component(i); + seqs[i] = av.getAlignment().getSequenceAt(i); } } - - ////////////////// - - xCombobox.select(0); - yCombobox.select(1); - zCombobox.select(2); - - top = pca.getM().rows - 1; - - Vector points = new Vector(); - float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); - - for (int i = 0; i < pca.getM().rows; i++) - { - SequencePoint sp = new SequencePoint(s[i], scores[i]); - points.addElement(sp); - } - - rc = new RotatableCanvas(av, points, pca.getM().rows); - - //rc.printPoints(); - + rc = new RotatableCanvas(av); add(rc, BorderLayout.CENTER); + Thread worker = new Thread(this); + worker.start(); + } + + /** + * DOCUMENT ME! + */ + public void run() + { + pca = new PCA(seqs); + pca.run(); + + // Now find the component coordinates + int ii = 0; + + while ((ii < seqs.length) && (seqs[ii] != null)) + { + ii++; + } + + double[][] comps = new double[ii][ii]; + + for (int i = 0; i < ii; i++) + { + if (pca.getEigenvalue(i) > 1e-4) + { + comps[i] = pca.component(i); + } + } + + ////////////////// + xCombobox.select(0); + yCombobox.select(1); + zCombobox.select(2); + + top = pca.getM().rows - 1; + + Vector points = new Vector(); + float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); + + for (int i = 0; i < pca.getM().rows; i++) + { + SequencePoint sp = new SequencePoint(seqs[i], scores[i]); + points.addElement(sp); + } + + rc.setPoints(points, pca.getM().rows); + rc.repaint(); + seqs = null; } void doDimensionChange() diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java index 25754cd..9fa7491 100755 --- a/src/jalview/appletgui/RotatableCanvas.java +++ b/src/jalview/appletgui/RotatableCanvas.java @@ -32,8 +32,6 @@ public class RotatableCanvas extends Panel implements MouseListener, MouseMotionListener, KeyListener -//RubberbandListener, -//SequenceSelectionListener { RotatableMatrix idmat = new RotatableMatrix(3, 3); RotatableMatrix objmat = new RotatableMatrix(3, 3); @@ -82,17 +80,19 @@ public class RotatableCanvas float scalefactor = 1; AlignViewport av; -// Controller controller; + public RotatableCanvas(AlignViewport av) + { + this.av = av; + } - public RotatableCanvas(AlignViewport av, - Vector points, int npoint) + public void setPoints(Vector points, int npoint) { this.points = points; this.npoint = npoint; this.av = av; PaintRefresher.Register(this, av.alignment); -// + prefsize = getPreferredSize(); orig = new float[npoint][3]; @@ -287,29 +287,38 @@ public class RotatableCanvas public void paint(Graphics g) { - //Only create the image at the beginning - - if ( (img == null) || (prefsize.width != getSize().width) || - (prefsize.height != getSize().height)) + if (points == null) + { + g.setFont(new Font("Verdana", Font.PLAIN, 18)); + g.drawString("Calculating PCA....", 20, getSize().height / 2); + } + else { - prefsize.width = getSize().width; - prefsize.height = getSize().height; - scale = findScale(); + //Only create the image at the beginning - + if ( (img == null) || (prefsize.width != getSize().width) || + (prefsize.height != getSize().height)) + { + prefsize.width = getSize().width; + prefsize.height = getSize().height; - // System.out.println("New scale = " + scale); - img = createImage(getSize().width, getSize().height); - ig = img.getGraphics(); + scale = findScale(); - } + // System.out.println("New scale = " + scale); + img = createImage(getSize().width, getSize().height); + ig = img.getGraphics(); - drawBackground(ig, Color.black); - drawScene(ig); - if (drawAxes == true) - { - drawAxes(ig); - } + } - g.drawImage(img, 0, 0, this); + drawBackground(ig, Color.black); + drawScene(ig); + if (drawAxes == true) + { + drawAxes(ig); + } + + g.drawImage(img, 0, 0, this); + } } public void drawAxes(Graphics g) diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 7bda65a..474a158 100755 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -42,6 +42,7 @@ public class PCAPanel extends GPCAPanel implements Runnable int top; RotatableCanvas rc; AlignViewport av; + SequenceI [] seqs; /** * Creates a new PCAPanel object. @@ -56,74 +57,78 @@ public class PCAPanel extends GPCAPanel implements Runnable if ((av.getSelectionGroup() != null) && (av.getSelectionGroup().getSize() > 3)) { - s = new Sequence[av.getSelectionGroup().getSize()]; + seqs = new Sequence[av.getSelectionGroup().getSize()]; for (int i = 0; i < s.length; i++) { - s[i] = av.getSelectionGroup().getSequenceAt(i); + seqs[i] = av.getSelectionGroup().getSequenceAt(i); } } if (s == null) { - s = new Sequence[av.getAlignment().getHeight()]; + seqs = new Sequence[av.getAlignment().getHeight()]; for (int i = 0; i < av.getAlignment().getHeight(); i++) { - s[i] = av.getAlignment().getSequenceAt(i); + seqs[i] = av.getAlignment().getSequenceAt(i); } } - //////////////////////This part was done in PCATHread originally. Is it too slow??? - pca = new PCA(s); - pca.run(); - // Now find the component coordinates - int ii = 0; - - while ((ii < s.length) && (s[ii] != null)) - { - ii++; - } - - double[][] comps = new double[ii][ii]; - - for (int i = 0; i < ii; i++) - { - if (pca.getEigenvalue(i) > 1e-4) - { - comps[i] = pca.component(i); - } - } - - ////////////////// - xCombobox.setSelectedIndex(0); - yCombobox.setSelectedIndex(1); - zCombobox.setSelectedIndex(2); - - top = pca.getM().rows - 1; - - Vector points = new Vector(); - float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); - - for (int i = 0; i < pca.getM().rows; i++) - { - SequencePoint sp = new SequencePoint(s[i], scores[i]); - points.addElement(sp); - } - - rc = new RotatableCanvas(av, points, pca.getM().rows); - - //rc.printPoints(); + rc = new RotatableCanvas(av); add(rc, BorderLayout.CENTER); + Thread worker = new Thread(this); + worker.start(); } + + /** * DOCUMENT ME! */ public void run() { - // do stuff + pca = new PCA(seqs); + pca.run(); + + // Now find the component coordinates + int ii = 0; + + while ((ii < seqs.length) && (seqs[ii] != null)) + { + ii++; + } + + double[][] comps = new double[ii][ii]; + + for (int i = 0; i < ii; i++) + { + if (pca.getEigenvalue(i) > 1e-4) + { + comps[i] = pca.component(i); + } + } + + ////////////////// + xCombobox.setSelectedIndex(0); + yCombobox.setSelectedIndex(1); + zCombobox.setSelectedIndex(2); + + top = pca.getM().rows - 1; + + Vector points = new Vector(); + float[][] scores = pca.getComponents(top - 1, top - 2, top - 3, 100); + + for (int i = 0; i < pca.getM().rows; i++) + { + SequencePoint sp = new SequencePoint(seqs[i], scores[i]); + points.addElement(sp); + } + + rc.setPoints(points, pca.getM().rows); + rc.repaint(); + seqs = null; } /** diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java index 460a99f..3fcfd3d 100755 --- a/src/jalview/gui/RotatableCanvas.java +++ b/src/jalview/gui/RotatableCanvas.java @@ -40,8 +40,6 @@ import javax.swing.*; */ public class RotatableCanvas extends JPanel implements MouseListener, MouseMotionListener, KeyListener -//RubberbandListener, -//SequenceSelectionListener { RotatableMatrix idmat = new RotatableMatrix(3, 3); RotatableMatrix objmat = new RotatableMatrix(3, 3); @@ -78,11 +76,15 @@ public class RotatableCanvas extends JPanel implements MouseListener, AlignViewport av; // Controller controller; - public RotatableCanvas(AlignViewport av, Vector points, int npoint) + public RotatableCanvas(AlignViewport av) + { + this.av = av; + } + + public void setPoints(Vector points, int npoint) { this.points = points; this.npoint = npoint; - this.av = av; ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); @@ -129,31 +131,13 @@ public class RotatableCanvas extends JPanel implements MouseListener, scale = findScale(); - // System.out.println("Scale factor = " + scale); addMouseListener(this); addKeyListener(this); - // if (getParent() != null) { - // getParent().addKeyListener(this); - //} addMouseMotionListener(this); - // Add rubberband - // rubberband = new RubberbandRectangle(this); - // rubberband.setActive(true); - // rubberband.addListener(this); } - /* public boolean handleSequenceSelectionEvent(SequenceSelectionEvent evt) { - redrawneeded = true; - repaint(); - return true; - } - - public void removeNotify() { - controller.removeListener(this); - super.removeNotify(); - }*/ public void initAxes() { for (int i = 0; i < 3; i++) @@ -313,18 +297,25 @@ public class RotatableCanvas extends JPanel implements MouseListener, */ public void paintComponent(Graphics g) { + if(points==null) + { + g.setFont(new Font("Verdana", Font.PLAIN, 18)); + g.drawString("Calculating PCA....", 20, getHeight()/2); + } + else + { //Only create the image at the beginning - - if ((img == null) || (prefsize.width != getWidth()) || - (prefsize.height != getHeight())) + if ( (img == null) || (prefsize.width != getWidth()) || + (prefsize.height != getHeight())) { - prefsize.width = getWidth(); - prefsize.height = getHeight(); + prefsize.width = getWidth(); + prefsize.height = getHeight(); - scale = findScale(); + scale = findScale(); - // System.out.println("New scale = " + scale); - img = createImage(getWidth(), getHeight()); - ig = img.getGraphics(); + // System.out.println("New scale = " + scale); + img = createImage(getWidth(), getHeight()); + ig = img.getGraphics(); } drawBackground(ig, Color.black); @@ -332,10 +323,11 @@ public class RotatableCanvas extends JPanel implements MouseListener, if (drawAxes == true) { - drawAxes(ig); + drawAxes(ig); } g.drawImage(img, 0, 0, this); + } } /** -- 1.7.10.2