[Jtreeview-cvs] jtreeview commit notification
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From: Alok S. <al...@us...> - 2005-02-07 04:56:19
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Update of /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv15258/src/edu/stanford/genetics/treeview/dendroview Modified Files: CharArrayDrawer.java CharColorSet.java DendroView.java GTRView.java KnnDendroView.java TreeDrawer.java CharDendroView.java ZoomView.java IntegerMap.java GlobalView.java LeftTreeDrawer.java InvertedTreeDrawer.java Log Message: fixed all javadoc warnings. Index: CharDendroView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/CharDendroView.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** CharDendroView.java 21 Dec 2004 03:28:11 -0000 1.6 --- CharDendroView.java 7 Feb 2005 04:55:33 -0000 1.7 *************** *** 51,55 **** * Constructor for the CharDendroView object * ! * @param viewFrame parent ViewFrame of CharDendroView * @param configNode node in which to store persistent configuration info (if desired) */ --- 51,55 ---- * Constructor for the CharDendroView object * ! * @param vFrame parent ViewFrame of CharDendroView * @param configNode node in which to store persistent configuration info (if desired) */ Index: GTRView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/GTRView.java,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -d -r1.16 -r1.17 *** GTRView.java 31 Jan 2005 14:25:12 -0000 1.16 --- GTRView.java 7 Feb 2005 04:55:33 -0000 1.17 *************** *** 98,110 **** /** ! * Set the selected node, update the TreeSelection and redraw * Should be called whenever the internal pointer to selected node * is changed. - * - * @param n The new node to be selected - * - * Does nothing if the node is already selected. */ - private void synchMap() { if ((selectedNode != null) && (geneSelection != null)) { --- 98,109 ---- /** ! * Synchronizes TreeSelection with selectedNode. ! * ! * sets the TreeSelection to reflect the span of the selected node. ! * sets the selected node of the TreeSelection to this node. ! * Notifies observers. * Should be called whenever the internal pointer to selected node * is changed. */ private void synchMap() { if ((selectedNode != null) && (geneSelection != null)) { Index: KnnDendroView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/KnnDendroView.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** KnnDendroView.java 21 Dec 2004 03:28:11 -0000 1.17 --- KnnDendroView.java 7 Feb 2005 04:55:33 -0000 1.18 *************** *** 49,53 **** * * @param tVModel model this KnnDendroView is to represent ! * @param viewFrame parent ViewFrame of KnnDendroView */ public KnnDendroView(KnnModel tVModel, ViewFrame vFrame) { --- 49,53 ---- * * @param tVModel model this KnnDendroView is to represent ! * @param vFrame parent ViewFrame of KnnDendroView */ public KnnDendroView(KnnModel tVModel, ViewFrame vFrame) { Index: DendroView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/DendroView.java,v retrieving revision 1.39 retrieving revision 1.40 diff -C2 -d -r1.39 -r1.40 *** DendroView.java 21 Dec 2004 03:28:11 -0000 1.39 --- DendroView.java 7 Feb 2005 04:55:33 -0000 1.40 *************** *** 55,59 **** * * @param tVModel model this DendroView is to represent ! * @param viewFrame parent ViewFrame of DendroView */ public DendroView(DataModel tVModel, ViewFrame vFrame) { --- 55,59 ---- * * @param tVModel model this DendroView is to represent ! * @param vFrame parent ViewFrame of DendroView */ public DendroView(DataModel tVModel, ViewFrame vFrame) { *************** *** 75,79 **** * @param tVModel model this DendroView is to represent * @param root Confignode to which to bind this DendroView ! * @param viewFrame parent ViewFrame of DendroView */ public DendroView(DataModel tVModel, ConfigNode root, ViewFrame vFrame) { --- 75,79 ---- * @param tVModel model this DendroView is to represent * @param root Confignode to which to bind this DendroView ! * @param vFrame parent ViewFrame of DendroView */ public DendroView(DataModel tVModel, ConfigNode root, ViewFrame vFrame) { Index: GlobalView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/GlobalView.java,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** GlobalView.java 21 Dec 2004 03:28:10 -0000 1.15 --- GlobalView.java 7 Feb 2005 04:55:33 -0000 1.16 *************** *** 120,124 **** * Get ArrayDrawer * ! * @param arrayDrawer The current ArrayDrawer */ public ArrayDrawer getArrayDrawer() { --- 120,124 ---- * Get ArrayDrawer * ! * @return The current ArrayDrawer */ public ArrayDrawer getArrayDrawer() { *************** *** 155,159 **** * get the xmapping for this view * ! * @param m the current mapping */ public MapContainer getXMap() {return xmap;} --- 155,159 ---- * get the xmapping for this view * ! * @return the current mapping */ public MapContainer getXMap() {return xmap;} *************** *** 162,166 **** * get the ymapping for this view * ! * @param m the current mapping */ public MapContainer getYMap() {return ymap;} --- 162,166 ---- * get the ymapping for this view * ! * @return the current mapping */ public MapContainer getYMap() {return ymap;} Index: ZoomView.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/ZoomView.java,v retrieving revision 1.17 retrieving revision 1.18 diff -C2 -d -r1.17 -r1.18 *** ZoomView.java 21 Dec 2004 03:28:11 -0000 1.17 --- ZoomView.java 7 Feb 2005 04:55:33 -0000 1.18 *************** *** 122,126 **** * Get ArrayDrawer * ! * @param arrayDrawer The current ArrayDrawer */ public ArrayDrawer getArrayDrawer() { --- 122,126 ---- * Get ArrayDrawer * ! * @return The current ArrayDrawer */ public ArrayDrawer getArrayDrawer() { *************** *** 153,157 **** * get the xmapping for this view * ! * @param m the current mapping */ public MapContainer getXMap() {return xmap;} --- 153,157 ---- * get the xmapping for this view * ! * @return the current mapping */ public MapContainer getXMap() {return xmap;} *************** *** 161,165 **** * get the ymapping for this view * ! * @param m the current mapping */ public MapContainer getYMap() {return ymap;} --- 161,165 ---- * get the ymapping for this view * ! * @return the current mapping */ public MapContainer getYMap() {return ymap;} Index: TreeDrawer.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/TreeDrawer.java,v retrieving revision 1.14 retrieving revision 1.15 diff -C2 -d -r1.14 -r1.15 *** TreeDrawer.java 21 Dec 2004 03:28:11 -0000 1.14 --- TreeDrawer.java 7 Feb 2005 04:55:33 -0000 1.15 *************** *** 261,268 **** * @param graphics The graphics object to draw on ! * @param corrMin The lower bound of minor axis to render ! * @param corrMax The upper bound of minor axis to render ! * @param indMin The lower bound of major axis to render ! * @param indMax The upper bound of major axis to render * @param dest Specifies Rectangle of pixels to draw to * @param selected A selected node --- 261,266 ---- * @param graphics The graphics object to draw on ! * @param xScaleEq Equation describing mapping from pixels to index ! * @param yScaleEq Equation describing mapping from pixels to index * @param dest Specifies Rectangle of pixels to draw to * @param selected A selected node *************** *** 308,318 **** * The constructor sets the variables * ! * @param index The index we are searching for ! ! * @param correlation The correlation we are searching for ! ! * @param weigh The relative weight to assign to ! * correlation. The distance function will be ! * sqrt((delta(corr) * weight) ^2 + (delta(index))^2) */ public IterativeClosestFinder(double ind, double corr, --- 306,312 ---- * The constructor sets the variables * ! * @param ind The index for which to search ! * @param corr The correlation for which to search ! * @param wei The relative weight to assign to correlation. The distance function will be sqrt((delta(corr) * weight) ^2 + (delta(index))^2) */ public IterativeClosestFinder(double ind, double corr, Index: CharArrayDrawer.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/CharArrayDrawer.java,v retrieving revision 1.6 retrieving revision 1.7 diff -C2 -d -r1.6 -r1.7 *** CharArrayDrawer.java 21 Dec 2004 03:28:11 -0000 1.6 --- CharArrayDrawer.java 7 Feb 2005 04:55:33 -0000 1.7 *************** *** 89,95 **** * Set the source of the data. * ! * @param headerInfo A HeaderInfo containing the column of aligned sequence * @param name The name of the column - * @param nodataValue a value to represent nodata */ public void setHeaderInfo(HeaderInfo info, String name) { --- 89,94 ---- * Set the source of the data. * ! * @param info A HeaderInfo containing the column of aligned sequence * @param name The name of the column */ public void setHeaderInfo(HeaderInfo info, String name) { Index: LeftTreeDrawer.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/LeftTreeDrawer.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** LeftTreeDrawer.java 21 Dec 2004 03:28:11 -0000 1.4 --- LeftTreeDrawer.java 7 Feb 2005 04:55:34 -0000 1.5 *************** *** 112,124 **** /** * The constructor sets the variables ! * * @param g The graphics object to print to ! ! * @param xScaleEq The equation to be applied to scale the ! * index of the nodes to graphics object ! ! * @param yscaleEq The equation to be applied to scale the ! * correlation of the nodes to the graphics object ! * maybe foreground color, selection color and node color should be options? */ --- 112,119 ---- /** * The constructor sets the variables ! * * @param g The graphics object to print to ! * @param xScaleEq The equation to be applied to scale the index of the nodes to graphics object ! * @param yScaleEq The equation to be applied to scale the correlation of the nodes to the graphics object * maybe foreground color, selection color and node color should be options? */ Index: InvertedTreeDrawer.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/InvertedTreeDrawer.java,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** InvertedTreeDrawer.java 21 Dec 2004 03:28:11 -0000 1.3 --- InvertedTreeDrawer.java 7 Feb 2005 04:55:34 -0000 1.4 *************** *** 112,116 **** * index of the nodes to graphics object ! * @param yscaleEq The equation to be applied to scale the * correlation of the nodes to the graphics object --- 112,116 ---- * index of the nodes to graphics object ! * @param yScaleEq The equation to be applied to scale the * correlation of the nodes to the graphics object Index: IntegerMap.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/IntegerMap.java,v retrieving revision 1.5 retrieving revision 1.6 diff -C2 -d -r1.5 -r1.6 *** IntegerMap.java 21 Dec 2004 03:28:11 -0000 1.5 --- IntegerMap.java 7 Feb 2005 04:55:33 -0000 1.6 *************** *** 37,45 **** protected ConfigNode root; - /** - * This constructor builds double from xml element - * - * @param element The xml element which represents this double - */ public IntegerMap() { --- 37,40 ---- *************** *** 75,79 **** /** ! * @param pixel pixel to find definitive index for. * @return index into array for that pixel */ --- 70,74 ---- /** ! * @param i pixel for which to find index * @return index into array for that pixel */ *************** *** 109,116 **** // subclasses implement actual mapping functions /** ! * @param indval the index for which we want the first pixel of * * @return first pixel corresponding to index - * note: if i == maxindex + 1, return the first pixel beyond end of max */ public abstract int getPixel(int i); --- 104,112 ---- // subclasses implement actual mapping functions /** ! * note: if i == maxindex + 1, return the first pixel beyond end of max ! * ! * @param i the index for which we want the first pixel of * * @return first pixel corresponding to index */ public abstract int getPixel(int i); *************** *** 159,163 **** public abstract int getViewableIndexes(); /** ! * @param p number of pixels which we can map to. The map will map * the index range to pixels 1 to n-1. */ --- 155,159 ---- public abstract int getViewableIndexes(); /** ! * @param i number of pixels which we can map to. The map will map * the index range to pixels 1 to n-1. */ *************** *** 170,175 **** * Set the range of pixels to map to * ! * @param np lower bound ! * @param mp upper bound */ public void setIndexRange(int i, int j) --- 166,171 ---- * Set the range of pixels to map to * ! * @param i lower bound ! * @param j upper bound */ public void setIndexRange(int i, int j) Index: CharColorSet.java =================================================================== RCS file: /cvsroot/jtreeview/LinkedView/src/edu/stanford/genetics/treeview/dendroview/CharColorSet.java,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** CharColorSet.java 21 Dec 2004 03:28:11 -0000 1.4 --- CharColorSet.java 7 Feb 2005 04:55:33 -0000 1.5 *************** *** 126,160 **** empty = decodeColor(root.getAttribute("empty", default_emptyColor)); name = root.getAttribute("name", default_name); ! } ! /** ! * Simple test program, prints out default color set using toString. ! * ! * if argument present, saves EisenFormat to specified file. ! * ! * @param argv optional arguments from command line. ! public final static void main(String[] argv) { ! ColorSet test = new ColorSet(); ! try { ! test.loadEisen(argv[0]); ! test.setName(argv[0]); ! System.out.println(test.toString()); ! } catch (Exception e) { ! System.out.println("Couldn't load file " + argv[0] + ": " + e); ! } ! if (argv.length > 1) { ! try { ! test.saveEisen(argv[1]); ! } catch (Exception e) { ! System.out.println("Couldn't save file " + argv[1] + ": " + e); ! } ! ! } ! } */ - - - /*inherit description*/ public String toString() { return "CharColorSet " + getName() + "\n" + --- 126,134 ---- empty = decodeColor(root.getAttribute("empty", default_emptyColor)); name = root.getAttribute("name", default_name); ! } /** ! * String represnetation of class. */ public String toString() { return "CharColorSet " + getName() + "\n" + |