aCGHViewer release notes: 2.16 fixed a bug in format handling 2.14 added the accormmodation of 4 colors 2.12 Added .view extension filter General clean up. 2.11 Fixed a number of issues:- Annotation misplacement if multiple zoomframes opened. Viewer sometimes uses default values for Y axis even though different values have been set. Printing is now set to landscape. Filename is also printed. Optimal results can be obtained if a margin of 0.25 inches is used on all edges. Print All command does not implement these improvements. Disabled checking of probe ids to determine if human or mouse data were being loaded. Users are now loading Affy data/probes from other organisms/ and the error dialogs were a bother. Memory minimum is now 256Mb. The application will run with less memory. This requirement is needed because users are starting to analyze 100k datasets. 2.06 Changed annotation circle and arrow to appear with ALT+mouse click. On Linux, the feature can be used by pressing the middle button instead of holding down the ALT button. 2.05 released with revised paper doesn't display annotations when ctrl+clicked on a data point in zoomframe. works ok on xp, not so well on w2k. On w2k, if multiple zoomframes are opened, then annotations from all zoomframes are shown on one 111605 Released as aCGHViewer 2.01 Fixed absolute value repainting bug. When new values were input, they weren't being incorporated into a new graph. propagated bug fix to mac verison. Better about box info for mac version. Included LGPL license file in CONFIG folder. updated user guide. Some wonky behaviour on windows noted - zoomout goes too far sometimes, printing problem from some machines -workaround is to not resize the main window from its default size. 110805 Released as aCGHViewer 2.0.jar, aCGHViewer 2.0.exe, aCGHViewer 2.0.App Splashscreen added. Added platform default look and feel. Filehistory in filechooser. Made expression data points blue - not true blue, but close. TODO Have to pick better HSB values. If website=ncbi, and probe id does not contain"RP11" or "RP23", the probe is sent to Unigene. This is meant to prevent expression probes from returning as 'not found' at the regular genome browser site. Turned off cross hairs. Printing works - Genomic view window can be any size and the figure is scaled to fit one page. Have to set landscape orientation and margins. Printing also doesn't print file name anymore. Fixed bug where probe id, and cytoband info would be null in combined graphs. This would resolve itself given time. Moved the zoompanel creation to an earlier time. Null bug still appears sporadically on one laptop. Have been unable to replicate. Data Points can be annotaed with tooltip info with ctrl+click. Mac version has been forked since JDK is only up to 1.4. In order to make annotations work, zoomframe explicitely declares some variable to be doubles, etc. Also, had to use Alt-click for annotations as ctrl-click brings up the context menu. 09/26/05 Released as aCGHViewer_1.9_gs.jar, aCGHViewer 1.9.exe, aCGHViewer 1.9 Tooltips now remain visible as long as cursor is on data point. Tooltips also appear faster. Changed file format to include and require header line. Header line should contain a title for each column of data. Fixed bug that opened empty genomic view when user cancelled out of conflict dialog. This occured only when previous data loading/display occured correctly. Fixed repainting bug. If absolute YAxis values were changed for one plot, the plot repainted. If values for second plot were also changed, it didn't repaint. Fixed mouse yaxis, repainting bug. 09/19/05 Released as aCGHViewer_1.85_gs.jar, aCGHViewer_1.85.exe, aCGHViewer User can launch 'breakpoint box' by holding down shift key while dragging mouse. Yellow rectangle is drawn and queries the genome browser website with the starting and ending x coordinates. User can select line or scatter plots. Changing plot preferences now also redraws zoom window. When zooming out, the maximum zoom out dimensions matches the Y axis preference chosen by user. Error dialog appears if user cancels out of choosing the expression data file during 'combined' dataset analysis. Error dialog appears if loading non-BAC data, just choose continue. Program hangs if log file in CONFIG folder does not have read/write permission. Released as aCGHView_1.7_gs.jar, aCGHView 1.7.exe, aCGHView User can now overlay expression data onto BAC data for 4 column (non-categorized) data. Initial genomic view shows only BAC data as squares. Expression data is displayed in zoom window as gray triangles. There is no tooltip cytoband information for expression data. Overlay expression graphs for 5 column data is not currently supported. User can now choose multiple files from one directory for simple graphs. Changing the Y Axis selection in options now redraws the current graph. User can now specify max and min Y axis values for absolute graph type. Default is 4 digits in total with one digit after the decimal point. The default filename on printed output is the BAC filename. For Linux, user can now launch browser launch from data point click. 07/18/05 Released as aCGHView_1.6_gs Program can now handle mouse data. Data format should be the same as human data format. Horizontal line at zero. Bad data dialog does not force user to quit application. Tooltip contains id,cytoband, value. Genomic view tabs can be closed. Required files are now named: human_cytobands.txt, human_entromeres.txt, mouse_cytobands.txt and they are contained in a config folder. The config folder needs to be in the same folder as aCGHView. Program no longer allows inappropriate zoomout from a zoom window (right-click>zoom out>both axes). 07/05/05 Released as aCGHView_1.5_gs Program displays dialog boxes when cytoband and centromere files are not detected. It can continue without these files. Program performs basic checks of data. Options menu item under Tools is now active. User can specify: Website Organism Graph "type". Absolute means that Y axis is set to -5 and +2 for all graphs. Chromosome Relative means that the Y axis is set to the max and min value that occurs within each chrosome. Experiment Relative means that the Y axis is set to the max and min value that occurs within that set of 24 chromosomes. Note that choices should be made before loading data. The program does not currently redraw graphs based on changed preferences. The zoom window now displays a drop-down list box containing chromosome numbers. Choosing another chromosome causes that chromosome to be displayed. The list box can be scrolled by using the scroll bar or by moving the mouse up or down while the button is pressed down. Menu options can now be chosen using keyboard shortcuts. For example, CTRL+o to open files. 06/20/05 Released as aCGHView_1.4_gs -.exe for windows -.jar for macintosh, unix Program requires two datafiles called cytobands.txt and centromeres.txt to be located in the same folder as the program. Program will fail without these files. Program now displays vertical line indicating centromere location. Tooltip displays bacid, and cytoband for each datapoint in zoom window. Program can now handle data in two formats: bacid, chr, center, value bacid, chr, center, value, category. Category values can be:- 1=no change, displayed as black, 2= down, displayed as green, 3= up, displayed as red. Missing values are treated as 1. Note that data file should not contain a title row or "NA" for missing values. 05/24/05 Released as aCGHview_gs_1.3.jar Program runs in one window (except for the zoom windows). New genomic views are shown as tabs in that one window. One zoom window per genomic view. Note that you now have to double click on the genomic view panel to get it to display in the zoom window. File name is used as identifier in tabs, zoom window title bars, footer when printed. Wait cursor is displayed when importing data. Y-axis is now absolute scale -2 to +5. FOCUS Focus is easier to get and zoom window now chooses nearest data item. Note that randomly clicking anywhere in the graph picks the nearest item. Crosshairs appear to show user which data item was sent to the browser. PRINTING Zoom window can be printed by right-clicking. Can also be saved Print command on genomic view allows user to choose page orientation, margin, printer etc. TWO dialogs pop up per print command. Print all command on genomic view silently prints to default printer using default settings. No user input is allowed. 05/11/05 1.2 Fixed problem with ZoomFrame. It retained c'some number that was first clicked for the entire session. If a different c'some was clicked, it still mapped to the first c'some. Reverted chr1,chr2 panels to anti-aliased. Users prefer anti-aliased. 05/01/05 0.2 Ping released as aCGHview_gs_1.1.jar Refactored classes. Added Tools menu item in first window. Turned off anti-aliasing in chr1,chr2 panels. Supposed to increase speed. User's preference? 04/25/05 version 0.1 Needs JDK 1.5 Don't run from windows desktop. Should be able to launch the program by double clicking. Comes up with window allowing user to open data file. Input file is required to be tab delimited with ".txt" extension. Data should be formatted as follows: col 1 = bac id col 2 = chromosome, formatted as "chr1" etc col 3 = center of bac col 4 = value, log2 ratio, etc. Only 1 col of data. Data should not be missing bac id. The data should start on the first line,i.e, no titles. Any rows with missing center location data is discarded. Genomic summary window shows all 24 chromosomes. All chromosomes except Y, share a common Y axis. ChrY has its own Y axis. Clicking on the chromosome plot launches a zoom window. User can zoom in on interesting data points by clicking and dragging downward. Click and drag up to zoom out. Zooming can also be done in the genomic summary window. However, on zoom out, the Y axis is reset to that chromosome's default. Launches a new browser window for each clone clicked. Zoom window can be saved as a graphics file by right-clicking.