From: hansonr Date: Tue, 29 Jan 2019 07:39:55 +0000 (-0600) Subject: Fetch Sequences...PDB - all tabs working X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~275 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b0038bd579e099546c767d98a8006f29f5f71905;hp=cfb555030705793c96221979835a7ef8e3d49e9d;p=jalview.git Fetch Sequences...PDB - all tabs working Could still be a problem with panels being moved to and from being content panes. --- diff --git a/optimization/full-profile-ENSG000000157764-to-display-chrome.txt b/optimization/full-profile-ENSG000000157764-to-display-chrome.txt new file mode 100644 index 0000000..ae9c4cc --- /dev/null +++ b/optimization/full-profile-ENSG000000157764-to-display-chrome.txt @@ -0,0 +1,511 @@ + Total new objects: 3207143 + +count exec(ms) +-------- -------- ------------------------------ +...2100182 ....-24750 undefined[] +....504006 ......2661 java.lang.StringBuilder +....436463 ......1022 java.util.HashMap.Node +....411205 .......708 jalview.datamodel.Annotation +....232907 .......323 Float +....215619 .......902 jalview.datamodel.features.FeatureStore$SearchCriterion$3 +....206107 .......370 java.awt.Color +....206007 .......387 Integer +....205602 .......863 jalview.datamodel.ResidueCount +....205602 .......427 jalview.datamodel.Profile +....172921 ......1119 java.util.ArrayList.Itr +....170025 .....-2281 Object[] +....139805 .......151 Long +....138605 .......377 swingjs.json.JSON.JSONList +....108563 .......372 java.util.HashMap +....108553 .....-1316 java.util.HashMap.Node[] +....107812 ......3263 jalview.datamodel.SequenceFeature +.....79143 .......375 java.util.ArrayList +.....61212 .......381 java.util.HashMap.EntryIterator +.....52231 .......467 java.util.HashMap.EntrySet +.....47590 .......294 swingjs.json.JSON.JSONMap +.....46224 ........94 swingjs.json.JSON.JSONList.ListIterator +......7084 .......187 jalview.datamodel.features.NCNode +......3870 ........10 jalview.analysis.AlignmentUtils.DnaVariant +......3051 ........30 java.awt.Dimension +......2153 ........14 java.beans.PropertyChangeEvent +......1567 .........4 jalview.datamodel.SequenceCursor +......1356 .........6 java.util.LinkedHashMap.Entry +......1329 ........46 jalview.datamodel.features.NCList +......1290 .......-16 java.util.ArrayList[] +.......687 .........4 java.util.Hashtable.Entry +.......684 .........5 jalview.datamodel.DBRefEntry +.......505 .........6 java.util.TreeMap.ValueIterator +.......479 .........2 javax.swing.event.EventListenerList +.......449 .........6 java.util.ArrayList.SubList +.......449 .........4 java.util.HashSet +.......449 .........4 java.util.ArrayList$SubList$1 +.......444 .........1 jalview.datamodel.HiddenCursorPosition +.......402 ........-5 java.lang.Class[] +.......383 .........4 javajs.util.Lst +.......346 .........1 java.awt.geom.AffineTransform +.......346 .........1 java.awt.BasicStroke +.......290 ........-4 java.beans.PropertyChangeListener[] +.......287 .........3 java.util.Hashtable.Enumerator +.......280 .........5 java.awt.Rectangle +.......276 .........4 java.util.TreeMap.EntryIterator +.......274 ........-5 java.awt.Component[] +.......261 .........2 java.beans.PropertyChangeSupport +.......261 .........1 java.beans.PropertyChangeSupport.PropertyChangeListenerMap +.......226 .........1 java.util.Collections.UnmodifiableSet +.......219 .........0 com.stevesoft.pat.StrPos +.......206 .........1 java.awt.AWTEventMulticaster +.......200 .........2 java.util.HashMap.KeySet +.......200 .........2 java.util.HashMap.KeyIterator +.......198 .........4 javax.swing.plaf.ComponentInputMapUIResource +.......187 .........2 java.util.Arrays.ArrayList +.......182 .........2 java.awt.event.ContainerEvent +.......176 ........-3 java.util.Hashtable.Entry[] +.......173 .........1 javax.swing.ActionMap +.......173 ........-2 javax.swing.KeyStroke[] +.......171 .........2 java.awt.Insets +.......169 .........2 javax.swing.JMenuItem.MenuItemFocusListener +.......169 .........2 javax.swing.AbstractButton.Handler +.......169 .........1 swingjs.plaf.ButtonListener +.......154 .........1 javax.swing.KeyboardManager.ComponentKeyStrokePair +.......138 .........1 jalview.datamodel.PDBEntry +.......136 .........1 java.util.Vector.Itr +.......130 .........1 javajs.util.SB +.......120 .........2 java.io.BufferedInputStream +.......120 .........1 java.io.ByteArrayInputStream +.......116 .........2 javax.swing.DefaultButtonModel +.......112 .........2 java.lang.StringBuffer +.......108 .........3 java.awt.EventDispatchThread$1 +.......100 .........1 jalview.datamodel.features.FeatureStore$SearchCriterion$2 +........99 .........1 javax.swing.event.ChangeEvent +........94 .......514 javax.swing.JMenuItem +........91 .........2 java.awt.event.MouseEvent +........88 .........2 java.util.Hashtable +........88 .........0 java.util.TreeMap.Entry +........77 .........0 javax.swing.ArrayTable +........72 .........2 jalview.datamodel.features.FeatureStore +........72 .........1 java.util.TreeMap +........69 ........-1 java.util.concurrent.ConcurrentHashMap.HashEntry[] +........67 .......277 jalview.datamodel.Sequence +........67 ........18 jalview.datamodel.features.SequenceFeatures +........66 .........2 java.net.URL +........64 .........1 javajs.util.AjaxURLConnection +........64 .........0 java.util.concurrent.ConcurrentHashMap.Segment +........63 ........-1 jalview.datamodel.SequenceGroup[] +........60 .........2 java.util.Collections$UnmodifiableCollection$1 +........60 .........0 javax.swing.SizeRequirements +........57 .........2 java.awt.EventDispatchThread +........57 .........1 java.awt.EventDispatchThread.HierarchyEventFilter +........54 .........3 swingjs.json.JSON.JSONReader +........53 .........1 javax.swing.JToggleButton.ToggleButtonModel +........53 .........1 java.util.ArrayList.ListItr +........53 ........-1 swingjs.api.js.DOMNode[] +........51 .........0 java.awt.EventQueueItem +........51 ........-1 jalview.datamodel.SequenceI[] +........44 .........0 jalview.util.LinkedIdentityHashSet.IdentityWrapper +........39 .........4 jalview.datamodel.HiddenColumnsCursor +........38 .........0 java.lang.StackTraceElement +........35 ........90 javax.swing.JCheckBoxMenuItem +........34 .........5 jalview.util.MapList +........33 .........2 jalview.ext.ensembl.EnsemblXref +........33 .........1 java.util.StringTokenizer +........33 .........1 jalview.datamodel.Sequence.DBModList +........33 .........0 jalview.renderer.ScaleRenderer.ScaleMark +........32 .........0 java.util.Collections.SynchronizedRandomAccessList +........31 .........0 java.lang.reflect.Constructor +........31 .........0 java.awt.Point +........31 .........0 com.stevesoft.pat.oneChar +........30 .........0 javax.swing.KeyStroke +........30 .........0 javax.swing.ComponentInputMap +........28 .........0 com.stevesoft.pat.patInt +........27 .........0 java.util.Vector +........24 .........1 javax.swing.DefaultSingleSelectionModel +........23 .........1 java.util.SubList$1 +........23 .........0 java.util.TreeMap.Values +........23 .........0 java.util.TreeMap.EntrySet +........23 .........0 java.util.AbstractList.ListItr +........23 .........0 jalview.datamodel.Mapping +........22 .........8 javax.swing.JPopupMenu +........22 .........5 javax.swing.JPopupMenu.Separator +........22 .........1 javax.swing.JMenu.MenuChangeListener +........22 .........1 java.util.TimSort +........22 .........1 java.util.RandomAccessSubList +........22 .........0 swingjs.plaf.JSPopupMenuUI.JSMenuKeyListener +........22 .........0 javax.swing.JMenu.WinListener +........21 ........16 javax.swing.JMenu +........21 .........1 jalview.ext.ensembl.EnsemblProtein +........21 .........1 jalview.ext.ensembl.EnsemblCdna +........20 .........0 java.awt.FlowLayout +........18 ........98 javax.swing.JRadioButtonMenuItem +........18 .........0 java.util.Formatter.Flags +........18 .........0 java.awt.event.ItemEvent +........18 .........0 java.awt.event.InvocationEvent +........18 .........0 java.awt.BorderLayout +........16 .........0 jalview.datamodel.features.FeatureAttributes.AttributeData +........15 .........5 javax.swing.JPanel +........15 .........0 javax.swing.JComponent$2 +........14 .......183 jalview.datamodel.Alignment +........14 .........8 jalview.datamodel.HiddenColumns +........14 .........1 java.util.LinkedList.ListItr +........14 .........1 jalview.schemes.JalviewColourScheme +........14 .........0 jalview.gui.ColourMenuHelper$3 +........14 .........0 jalview.datamodel.HiddenSequences +........13 .........1 java.util.LinkedHashMap +........13 .........1 jalview.util.ReverseListIterator +........12 .........0 java.awt.AlphaComposite +........11 .........0 jalview.jbgui.GAlignFrame$1 +........10 .........0 java.util.BitSet +........10 .........0 java.awt.geom.Rectangle2D.Float +........10 .........0 java.awt.Color[] +.........9 .........1 java.util.LinkedHashMap.LinkedEntrySet +.........9 .........0 java.util.LinkedHashMap.LinkedEntryIterator +.........8 .........1 java.util.Formatter.FormatSpecifier +.........8 .........0 java.util.Formatter.FixedString +.........8 .........0 java.awt.Font +.........8 .........0 com.stevesoft.pat.Pthings +.........7 .........0 javax.swing.text.Segment +.........7 .........0 java.util.concurrent.ConcurrentHashMap.HashEntry +.........7 .........0 java.awt.event.ComponentEvent +.........7 .........0 com.stevesoft.pat.Bracket +.........6 .........0 swingjs.JSFontMetrics +.........6 .........0 javax.swing.SizeRequirements[] +.........6 .........0 javax.swing.DefaultBoundedRangeModel +.........6 .........0 java.util.Formatter.FormatString[] +.........6 .........0 java.util.AbstractList.Itr +.........6 .........0 jalview.datamodel.Range +.........6 .........0 com.stevesoft.pat.SubMark +.........6 .........0 com.stevesoft.pat.Range +.........6 .........0 com.stevesoft.pat.OrMark +.........6 .........0 com.stevesoft.pat.FastMulti +.........5 .........1 swingjs.JSGraphics2D +.........5 .........0 sun.java2d.StateTrackableDelegate +.........5 .........0 javax.swing.event.InternalFrameEvent +.........5 .........0 java.awt.RenderingHints +.........5 .........0 jalview.renderer.ResidueShader +.........5 .........0 Boolean +.........4 .........2 javax.swing.JLabel +.........4 .........1 java.util.concurrent.ConcurrentHashMap +.........4 .........1 jalview.analysis.AnnotationSorter +.........4 .........0 sun.java2d.StateTrackable.State +.........4 .........0 javax.swing.JScrollBar.ModelListener +.........4 .........0 java.util.concurrent.ConcurrentHashMap.Segment[] +.........4 .........0 java.awt.geom.RectIterator +.........4 .........0 java.awt.event.AdjustmentEvent +.........4 .........0 jalview.ext.ensembl.EnsemblSeqProxy.EnsemblSeqType +.........4 .........0 jalview.analysis.AnnotationSorter$3 +.........4 .........0 jalview.analysis.AnnotationSorter$2 +.........4 .........0 jalview.analysis.AnnotationSorter$1 +.........4 .........0 com.stevesoft.pat.End +.........4 ........-2 jalview.datamodel.Annotation[] +.........3 ........81 java.awt.image.BufferedImage +.........3 .........9 java.awt.image.DataBufferInt +.........3 .........5 java.awt.image.DirectColorModel +.........3 .........0 swingjs.JSToolkit$1 +.........3 .........0 sun.font.FontDesignMetrics.KeyReference +.........3 .........0 sun.font.FontDesignMetrics +.........3 .........0 javax.swing.ButtonGroup +.........3 .........0 java.util.regex.Matcher +.........3 .........0 java.util.Collections.SynchronizedSet +.........3 .........0 java.awt.image.SinglePixelPackedSampleModel +.........3 .........0 java.awt.GridLayout +.........3 .........0 jalview.schemes.NucleotideColourScheme +.........3 .........0 jalview.renderer.ScaleRenderer +.........3 .........0 jalview.gui.AnnotationPanel.DragMode +.........3 .........0 jalview.datamodel.features.FeatureAttributes.Datatype +.........3 .........0 jalview.datamodel.VisibleContigsIterator +.........3 .........0 jalview.datamodel.StartRegionIterator +.........3 .........0 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder +.........2 .........8 javax.swing.JScrollBar +.........2 .........7 javax.swing.JScrollPane.ScrollBar +.........2 .........7 javax.swing.JProgressBar +.........2 .........2 java.lang.IndexOutOfBoundsException +.........2 .........2 com.stevesoft.pat.Regex +.........2 .........1 jalview.datamodel.AlignmentAnnotation +.........2 .........0 javax.swing.text.AbstractDocument.DefaultDocumentEvent +.........2 .........0 javax.swing.event.UndoableEditEvent +.........2 .........0 javax.swing.border.LineBorder +.........2 .........0 javax.swing.JProgressBar.ModelListener +.........2 .........0 java.util.LinkedHashMap.LinkedValues +.........2 .........0 java.util.LinkedHashMap.LinkedValueIterator +.........2 .........0 java.util.IdentityHashMap.KeyIterator +.........2 .........0 java.util.Hashtable.KeySet +.........2 .........0 java.util.Collections.SynchronizedCollection +.........2 .........0 java.util.Collections.SingletonList +.........2 .........0 java.util.Collections$1 +.........2 .........0 java.util.ArrayDeque +.........2 .........0 java.lang.Thread +.........2 .........0 java.lang.StackTraceElement[] +.........2 .........0 java.awt.geom.Path2D.Float.CopyIterator +.........2 .........0 java.awt.geom.Path2D.Float +.........2 .........0 java.awt.event.ActionEvent +.........2 .........0 java.awt.Container +.........2 .........0 jalview.util.IntRangeComparator +.........2 .........0 jalview.io.SequenceAnnotationReport +.........2 .........0 jalview.gui.AlignmentPanel[] +.........2 .........0 jalview.ext.ensembl.EnsemblSequenceFetcher.EnsemblFeatureType[] +.........2 .........0 jalview.ext.ensembl.EnsemblLookup +.........2 .........0 jalview.datamodel.features.RangeComparator +.........2 .........0 jalview.datamodel.SearchResults +.........2 .........0 jalview.datamodel.AlignmentAnnotation[] +.........2 .........0 jalview.controller.AlignViewController +.........2 .........0 com.stevesoft.pat.patInf +.........2 .........0 com.stevesoft.pat.Rthings +.........2 .........0 com.stevesoft.pat.Or +.........2 .........0 com.stevesoft.pat.NullPattern +.........1 .....14506 jalview.gui.AlignFrame +.........1 ......1341 jalview.gui.AlignViewport +.........1 .......249 jalview.gui.AlignmentPanel +.........1 ........85 jalview.gui.SeqPanel +.........1 ........84 jalview.schemes.ColourSchemes +.........1 ........53 jalview.gui.SeqCanvas +.........1 ........26 jalview.gui.IdPanel +.........1 ........13 javax.swing.JTabbedPane +.........1 ........11 jalview.io.FileFormats +.........1 ........10 jalview.gui.FeatureRenderer +.........1 .........9 javax.swing.JScrollPane +.........1 .........9 javax.swing.JInternalFrame.JDesktopIcon +.........1 .........8 jalview.datamodel.ColumnSelection.IntList +.........1 .........8 jalview.datamodel.ColumnSelection +.........1 .........7 sun.awt.image.SunWritableRaster$1 +.........1 .........7 jalview.gui.AnnotationPanel +.........1 .........5 javax.swing.JToolTip +.........1 .........4 jalview.jbgui.GAlignFrame$72 +.........1 .........3 jalview.gui.SequenceRenderer +.........1 .........3 jalview.ext.ensembl.EnsemblLookup$1 +.........1 .........2 javax.swing.JRootPane +.........1 .........2 jalview.io.gff.SequenceOntologyLite +.........1 .........2 jalview.gui.ViewSelectionMenu +.........1 .........1 swingjs.JSKeyEvent +.........1 .........1 javax.swing.text.GapContent.RemoveUndo +.........1 .........1 javax.swing.JViewport +.........1 .........1 javax.swing.JMenuBar +.........1 .........1 jalview.util.LinkedIdentityHashSet$1 +.........1 .........1 jalview.gui.ScalePanel +.........1 .........1 jalview.gui.IdwidthAdjuster +.........1 .........1 jalview.gui.IdCanvas +.........1 .........1 jalview.gui.AnnotationLabels +.........1 .........0 swingjs.plaf.Resizer +.........1 .........0 swingjs.plaf.LazyActionMap +.........1 .........0 swingjs.plaf.JSTabbedPaneUI.TabbedPaneLayout +.........1 .........0 swingjs.plaf.JSTabbedPaneUI.Handler +.........1 .........0 swingjs.plaf.JSScrollPaneUI.Handler +.........1 .........0 swingjs.plaf.JSMenuBarUI.Handler +.........1 .........0 swingjs.plaf.JSInternalFrameUI.Handler +.........1 .........0 swingjs.plaf.DefaultMenuLayout +.........1 .........0 swingjs.JSMouse +.........1 .........0 swingjs.JSFrameViewer +.........1 .........0 sun.java2d.StateTrackable.State[] +.........1 .........0 javax.swing.text.GapContent.UndoPosRef +.........1 .........0 javax.swing.text.GapContent.InsertUndo +.........1 .........0 javax.swing.plaf.basic.BasicBorders.MarginBorder +.........1 .........0 javax.swing.ScrollPaneLayout.UIResource +.........1 .........0 javax.swing.JViewport.ViewListener +.........1 .........0 javax.swing.JTabbedPane.ModelListener +.........1 .........0 javax.swing.JRootPane.RootLayout +.........1 .........0 javax.swing.JRootPane$1 +.........1 .........0 javax.swing.JLayeredPane +.........1 .........0 javax.swing.JComponent.IntVector +.........1 .........0 javajs.util.AjaxURLStreamHandler +.........1 .........0 javajs.api.JSFunction[] +.........1 .........0 java.util.concurrent.locks.ReentrantReadWriteLock.WriteLock +.........1 .........0 java.util.concurrent.locks.ReentrantReadWriteLock.ReadLock +.........1 .........0 java.util.concurrent.locks.ReentrantReadWriteLock +.........1 .........0 java.util.concurrent.ConcurrentHashMap.KeySet +.........1 .........0 java.util.concurrent.ConcurrentHashMap.KeyIterator +.........1 .........0 java.util.LinkedHashMap.LinkedKeySet +.........1 .........0 java.util.LinkedHashMap.LinkedKeyIterator +.........1 .........0 java.util.Hashtable.ValueCollection +.........1 .........0 java.util.Hashtable.EntrySet +.........1 .........0 java.util.Collections.UnmodifiableRandomAccessList +.........1 .........0 java.util.Collections.SynchronizedMap +.........1 .........0 java.util.Collections.EmptyIterator +.........1 .........0 java.util.Collections.EmptyEnumeration +.........1 .........0 java.lang.Thread[] +.........1 .........0 java.awt.event.WindowEvent +.........1 .........0 java.awt.event.FocusEvent +.........1 .........0 java.awt.dnd.DropTargetContext +.........1 .........0 java.awt.dnd.DropTarget +.........1 .........0 java.awt.color.ColorSpace +.........1 .........0 java.awt.Rectangle[] +.........1 .........0 java.awt.LightweightDispatcher +.........1 .........0 jalview.workers.ConsensusThread +.........1 .........0 jalview.workers.AlignCalcManager +.........1 .........0 jalview.viewmodel.styles.ViewStyle +.........1 .........0 jalview.viewmodel.seqfeatures.FeaturesDisplayed +.........1 .........0 jalview.viewmodel.ViewportRanges +.........1 .........0 jalview.util.LinkedIdentityHashSet +.........1 .........0 jalview.schemes.JalviewColourScheme[] +.........1 .........0 jalview.schemes.Consensus[] +.........1 .........0 jalview.renderer.ResidueColourFinder +.........1 .........0 jalview.renderer.AnnotationRenderer +.........1 .........0 jalview.jbgui.GAlignFrame$99 +.........1 .........0 jalview.jbgui.GAlignFrame$98 +.........1 .........0 jalview.jbgui.GAlignFrame$97 +.........1 .........0 jalview.jbgui.GAlignFrame$96 +.........1 .........0 jalview.jbgui.GAlignFrame$95 +.........1 .........0 jalview.jbgui.GAlignFrame$94 +.........1 .........0 jalview.jbgui.GAlignFrame$93 +.........1 .........0 jalview.jbgui.GAlignFrame$92 +.........1 .........0 jalview.jbgui.GAlignFrame$91 +.........1 .........0 jalview.jbgui.GAlignFrame$90 +.........1 .........0 jalview.jbgui.GAlignFrame$9 +.........1 .........0 jalview.jbgui.GAlignFrame$89 +.........1 .........0 jalview.jbgui.GAlignFrame$88 +.........1 .........0 jalview.jbgui.GAlignFrame$87 +.........1 .........0 jalview.jbgui.GAlignFrame$86 +.........1 .........0 jalview.jbgui.GAlignFrame$85 +.........1 .........0 jalview.jbgui.GAlignFrame$84 +.........1 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jalview.jbgui.GAlignFrame$65 +.........1 .........0 jalview.jbgui.GAlignFrame$64 +.........1 .........0 jalview.jbgui.GAlignFrame$63 +.........1 .........0 jalview.jbgui.GAlignFrame$62 +.........1 .........0 jalview.jbgui.GAlignFrame$61 +.........1 .........0 jalview.jbgui.GAlignFrame$60 +.........1 .........0 jalview.jbgui.GAlignFrame$6 +.........1 .........0 jalview.jbgui.GAlignFrame$59 +.........1 .........0 jalview.jbgui.GAlignFrame$58 +.........1 .........0 jalview.jbgui.GAlignFrame$57 +.........1 .........0 jalview.jbgui.GAlignFrame$56 +.........1 .........0 jalview.jbgui.GAlignFrame$55 +.........1 .........0 jalview.jbgui.GAlignFrame$54 +.........1 .........0 jalview.jbgui.GAlignFrame$53 +.........1 .........0 jalview.jbgui.GAlignFrame$52 +.........1 .........0 jalview.jbgui.GAlignFrame$51 +.........1 .........0 jalview.jbgui.GAlignFrame$50 +.........1 .........0 jalview.jbgui.GAlignFrame$5 +.........1 .........0 jalview.jbgui.GAlignFrame$49 +.........1 .........0 jalview.jbgui.GAlignFrame$48 +.........1 .........0 jalview.jbgui.GAlignFrame$47 +.........1 .........0 jalview.jbgui.GAlignFrame$46 +.........1 .........0 jalview.jbgui.GAlignFrame$45 +.........1 .........0 jalview.jbgui.GAlignFrame$44 +.........1 .........0 jalview.jbgui.GAlignFrame$43 +.........1 .........0 jalview.jbgui.GAlignFrame$42 +.........1 .........0 jalview.jbgui.GAlignFrame$41 +.........1 .........0 jalview.jbgui.GAlignFrame$40 +.........1 .........0 jalview.jbgui.GAlignFrame$4 +.........1 .........0 jalview.jbgui.GAlignFrame$39 +.........1 .........0 jalview.jbgui.GAlignFrame$38 +.........1 .........0 jalview.jbgui.GAlignFrame$37 +.........1 .........0 jalview.jbgui.GAlignFrame$36 +.........1 .........0 jalview.jbgui.GAlignFrame$35 +.........1 .........0 jalview.jbgui.GAlignFrame$34 +.........1 .........0 jalview.jbgui.GAlignFrame$33 +.........1 .........0 jalview.jbgui.GAlignFrame$32 +.........1 .........0 jalview.jbgui.GAlignFrame$31 +.........1 .........0 jalview.jbgui.GAlignFrame$30 +.........1 .........0 jalview.jbgui.GAlignFrame$3 +.........1 .........0 jalview.jbgui.GAlignFrame$29 +.........1 .........0 jalview.jbgui.GAlignFrame$28 +.........1 .........0 jalview.jbgui.GAlignFrame$27 +.........1 .........0 jalview.jbgui.GAlignFrame$26 +.........1 .........0 jalview.jbgui.GAlignFrame$25 +.........1 .........0 jalview.jbgui.GAlignFrame$24 +.........1 .........0 jalview.jbgui.GAlignFrame$23 +.........1 .........0 jalview.jbgui.GAlignFrame$22 +.........1 .........0 jalview.jbgui.GAlignFrame$21 +.........1 .........0 jalview.jbgui.GAlignFrame$20 +.........1 .........0 jalview.jbgui.GAlignFrame$2 +.........1 .........0 jalview.jbgui.GAlignFrame$19 +.........1 .........0 jalview.jbgui.GAlignFrame$18 +.........1 .........0 jalview.jbgui.GAlignFrame$17 +.........1 .........0 jalview.jbgui.GAlignFrame$16 +.........1 .........0 jalview.jbgui.GAlignFrame$15 +.........1 .........0 jalview.jbgui.GAlignFrame$14 +.........1 .........0 jalview.jbgui.GAlignFrame$13 +.........1 .........0 jalview.jbgui.GAlignFrame$121 +.........1 .........0 jalview.jbgui.GAlignFrame$120 +.........1 .........0 jalview.jbgui.GAlignFrame$12 +.........1 .........0 jalview.jbgui.GAlignFrame$119 +.........1 .........0 jalview.jbgui.GAlignFrame$118 +.........1 .........0 jalview.jbgui.GAlignFrame$117 +.........1 .........0 jalview.jbgui.GAlignFrame$116 +.........1 .........0 jalview.jbgui.GAlignFrame$115 +.........1 .........0 jalview.jbgui.GAlignFrame$114 +.........1 .........0 jalview.jbgui.GAlignFrame$113 +.........1 .........0 jalview.jbgui.GAlignFrame$112 +.........1 .........0 jalview.jbgui.GAlignFrame$111 +.........1 .........0 jalview.jbgui.GAlignFrame$110 +.........1 .........0 jalview.jbgui.GAlignFrame$11 +.........1 .........0 jalview.jbgui.GAlignFrame$109 +.........1 .........0 jalview.jbgui.GAlignFrame$108 +.........1 .........0 jalview.jbgui.GAlignFrame$107 +.........1 .........0 jalview.jbgui.GAlignFrame$106 +.........1 .........0 jalview.jbgui.GAlignFrame$105 +.........1 .........0 jalview.jbgui.GAlignFrame$104 +.........1 .........0 jalview.jbgui.GAlignFrame$103 +.........1 .........0 jalview.jbgui.GAlignFrame$102 +.........1 .........0 jalview.jbgui.GAlignFrame$101 +.........1 .........0 jalview.jbgui.GAlignFrame$100 +.........1 .........0 jalview.jbgui.GAlignFrame$10 +.........1 .........0 jalview.io.SequenceAnnotationReport$1 +.........1 .........0 jalview.io.FileFormat[] +.........1 .........0 jalview.io.FileFormat$9 +.........1 .........0 jalview.io.FileFormat$8 +.........1 .........0 jalview.io.FileFormat$7 +.........1 .........0 jalview.io.FileFormat$6 +.........1 .........0 jalview.io.FileFormat$5 +.........1 .........0 jalview.io.FileFormat$4 +.........1 .........0 jalview.io.FileFormat$3 +.........1 .........0 jalview.io.FileFormat$2 +.........1 .........0 jalview.io.FileFormat$19 +.........1 .........0 jalview.io.FileFormat$18 +.........1 .........0 jalview.io.FileFormat$17 +.........1 .........0 jalview.io.FileFormat$16 +.........1 .........0 jalview.io.FileFormat$15 +.........1 .........0 jalview.io.FileFormat$14 +.........1 .........0 jalview.io.FileFormat$13 +.........1 .........0 jalview.io.FileFormat$12 +.........1 .........0 jalview.io.FileFormat$11 +.........1 .........0 jalview.io.FileFormat$10 +.........1 .........0 jalview.io.FileFormat$1 +.........1 .........0 jalview.gui.ViewSelectionMenu$1 +.........1 .........0 jalview.gui.ProgressBar +.........1 .........0 jalview.gui.Desktop$13 +.........1 .........0 jalview.gui.Desktop$12 +.........1 .........0 jalview.gui.Desktop$11 +.........1 .........0 jalview.gui.ColourMenuHelper$4 +.........1 .........0 jalview.gui.ColourMenuHelper$1 +.........1 .........0 jalview.gui.AnnotationPanel.DragMode[] +.........1 .........0 jalview.gui.AlignmentPanel$2 +.........1 .........0 jalview.gui.AlignmentPanel$1 +.........1 .........0 jalview.gui.AlignFrame$5 +.........1 .........0 jalview.gui.AlignFrame$4 +.........1 .........0 jalview.gui.AlignFrame$3 +.........1 .........0 jalview.gui.AlignFrame$20 +.........1 .........0 jalview.gui.AlignFrame$2 +.........1 .........0 jalview.gui.AlignFrame$1 +.........1 .........0 jalview.ext.ensembl.EnsemblSeqProxy.EnsemblSeqType[] +.........1 .........0 jalview.ext.ensembl.EnsemblGene$1$2 +.........1 .........0 jalview.ext.ensembl.EnsemblGene$1$1 +.........1 .........0 jalview.ext.ensembl.EnsemblGene$1 +.........1 .........0 jalview.ext.ensembl.EnsemblFeatures +.........1 .........0 jalview.datamodel.features.SequenceFeatures$2 +.........1 .........0 jalview.datamodel.features.SequenceFeatures$1 +.........1 .........0 jalview.datamodel.features.FeatureAttributes.Datatype[] +.........1 .........0 jalview.datamodel.features.FeatureAttributes$1 +.........1 .........0 jalview.datamodel.features.FeatureAttributes +.........1 .........0 jalview.datamodel.Profiles +.........1 .........0 jalview.analysis.CrossRef +.........1 .........0 jalview.analysis.CodonComparator +.........1 .........0 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder[] +.........1 ........-1 jalview.datamodel.ProfileI[] +...5993224 .....61225 \ No newline at end of file diff --git a/optimization/full-profile-ENSG000000157764-to-display-ff.txt b/optimization/full-profile-ENSG000000157764-to-display-ff.txt new file mode 100644 index 0000000..0d48473 --- /dev/null +++ b/optimization/full-profile-ENSG000000157764-to-display-ff.txt @@ -0,0 +1,514 @@ +"run Clazz.startProfiling() first + + Total new objects: 3208398 + +count exec(ms) +-------- -------- ------------------------------ +...2100232 ....-40921 undefined[] +....504006 .....12402 java.lang.StringBuilder +....436605 ......3414 java.util.HashMap.Node +....411205 ......2841 jalview.datamodel.Annotation +....232907 ......1122 Float +....215619 ......2440 jalview.datamodel.features.FeatureStore$SearchCriterion$3 +....206107 ......1241 java.awt.Color +....206007 ......1059 Integer +....205602 ......3110 jalview.datamodel.ResidueCount +....205602 ......1697 jalview.datamodel.Profile +....172921 ......3075 java.util.ArrayList.Itr +....170314 .....-3144 Object[] +....139806 .......457 Long +....138605 ......1033 swingjs.json.JSON.JSONList +....108563 ......1065 java.util.HashMap +....108553 .....-2025 java.util.HashMap.Node[] +....107812 ......9397 jalview.datamodel.SequenceFeature +.....79143 ......1124 java.util.ArrayList +.....61212 ......1423 java.util.HashMap.EntryIterator +.....52231 ......1485 java.util.HashMap.EntrySet +.....47591 .......876 swingjs.json.JSON.JSONMap +.....46224 .......266 swingjs.json.JSON.JSONList.ListIterator +......7084 .......450 jalview.datamodel.features.NCNode +......3870 ........33 jalview.analysis.AlignmentUtils.DnaVariant +......3076 ........96 java.awt.Dimension +......2153 ........43 java.beans.PropertyChangeEvent +......1561 ........13 jalview.datamodel.SequenceCursor +......1356 ........18 java.util.LinkedHashMap.Entry +......1329 .......105 jalview.datamodel.features.NCList +......1290 .......-22 java.util.ArrayList[] +.......687 .........9 java.util.Hashtable.Entry +.......684 ........16 jalview.datamodel.DBRefEntry +.......526 ........16 javajs.util.Lst +.......505 ........21 java.util.TreeMap.ValueIterator +.......479 .........9 javax.swing.event.EventListenerList +.......449 ........19 java.util.HashSet +.......449 .........9 java.util.ArrayList$SubList$1 +.......449 .........8 java.util.ArrayList.SubList +.......440 .........0 jalview.datamodel.HiddenCursorPosition +.......402 ........-8 java.lang.Class[] +.......346 .........4 java.awt.geom.AffineTransform +.......346 .........4 java.awt.BasicStroke +.......325 ........28 java.awt.EventDispatchThread$1 +.......290 ........-7 java.beans.PropertyChangeListener[] +.......287 ........11 java.util.Hashtable.Enumerator +.......280 .........5 java.awt.Rectangle +.......276 .........7 java.util.TreeMap.EntryIterator +.......274 ........-7 java.awt.Component[] +.......261 ........10 java.beans.PropertyChangeSupport +.......261 .........6 java.beans.PropertyChangeSupport.PropertyChangeListenerMap +.......226 .........3 java.util.Collections.UnmodifiableSet +.......219 .........1 com.stevesoft.pat.StrPos +.......206 .........5 java.awt.AWTEventMulticaster +.......200 .........5 java.util.HashMap.KeySet +.......200 .........5 java.util.HashMap.KeyIterator +.......199 ........35 java.awt.EventDispatchThread +.......199 ........17 java.awt.EventDispatchThread.HierarchyEventFilter +.......198 .........2 javax.swing.plaf.ComponentInputMapUIResource +.......187 .........3 java.util.Arrays.ArrayList +.......182 ........14 java.awt.event.ContainerEvent +.......176 ........-7 java.util.Hashtable.Entry[] +.......173 .........2 javax.swing.ActionMap +.......173 ........-5 javax.swing.KeyStroke[] +.......171 .........3 java.awt.Insets +.......169 .........6 javax.swing.AbstractButton.Handler +.......169 .........5 javax.swing.JMenuItem.MenuItemFocusListener +.......169 .........2 swingjs.plaf.ButtonListener +.......154 .........4 javax.swing.KeyboardManager.ComponentKeyStrokePair +.......145 ........14 java.awt.event.MouseEvent +.......138 .........1 jalview.datamodel.PDBEntry +.......136 .........5 java.util.Vector.Itr +.......132 .........2 javajs.util.SB +.......126 .........3 java.awt.EventQueueItem +.......122 .........6 java.io.ByteArrayInputStream +.......122 .........6 java.io.BufferedInputStream +.......116 .........1 javax.swing.DefaultButtonModel +.......112 .........6 java.lang.StringBuffer +.......100 .........6 jalview.datamodel.features.FeatureStore$SearchCriterion$2 +........99 .........2 javax.swing.event.ChangeEvent +........94 .......690 javax.swing.JMenuItem +........88 .........3 java.util.Hashtable +........88 .........0 java.util.TreeMap.Entry +........77 .........1 javax.swing.ArrayTable +........72 .........8 jalview.datamodel.features.FeatureStore +........72 .........1 java.util.TreeMap +........69 ........-1 java.util.concurrent.ConcurrentHashMap.HashEntry[] +........67 .......176 jalview.datamodel.Sequence +........67 ........15 jalview.datamodel.features.SequenceFeatures +........67 .........7 java.net.URL +........65 .........1 javajs.util.AjaxURLConnection +........64 .........1 java.util.concurrent.ConcurrentHashMap.Segment +........63 ........-2 jalview.datamodel.SequenceGroup[] +........60 .........4 java.util.Collections$UnmodifiableCollection$1 +........60 .........0 javax.swing.SizeRequirements +........55 .......163 swingjs.json.JSON.JSONReader +........53 .........5 java.util.ArrayList.ListItr +........53 .........4 javax.swing.JToggleButton.ToggleButtonModel +........53 ........-2 swingjs.api.js.DOMNode[] +........51 ........-2 jalview.datamodel.SequenceI[] +........44 .........2 jalview.util.LinkedIdentityHashSet.IdentityWrapper +........39 .........5 jalview.datamodel.HiddenColumnsCursor +........38 .........1 java.lang.StackTraceElement +........35 .......169 javax.swing.JCheckBoxMenuItem +........34 ........11 jalview.util.MapList +........33 .........5 java.util.StringTokenizer +........33 .........5 jalview.datamodel.Sequence.DBModList +........33 .........2 jalview.renderer.ScaleRenderer.ScaleMark +........33 .........2 jalview.ext.ensembl.EnsemblXref +........32 .........1 java.util.Collections.SynchronizedRandomAccessList +........31 .........3 java.awt.event.ComponentEvent +........31 .........2 com.stevesoft.pat.oneChar +........31 .........1 java.lang.reflect.Constructor +........31 .........0 java.awt.Point +........30 .........0 javax.swing.KeyStroke +........30 .........0 javax.swing.ComponentInputMap +........28 .........1 com.stevesoft.pat.patInt +........27 .........1 java.util.Vector +........24 .........1 javax.swing.DefaultSingleSelectionModel +........23 .........5 java.util.SubList$1 +........23 .........3 java.util.AbstractList.ListItr +........23 .........3 jalview.datamodel.Mapping +........23 .........2 java.util.TreeMap.EntrySet +........23 .........1 java.util.TreeMap.Values +........22 ........21 javax.swing.JPopupMenu +........22 ........14 javax.swing.JPopupMenu.Separator +........22 .........2 javax.swing.JMenu.WinListener +........22 .........2 javax.swing.JMenu.MenuChangeListener +........22 .........2 java.util.TimSort +........22 .........1 java.util.RandomAccessSubList +........22 .........0 swingjs.plaf.JSPopupMenuUI.JSMenuKeyListener +........21 ........41 javax.swing.JMenu +........21 .........2 jalview.ext.ensembl.EnsemblProtein +........21 .........0 jalview.ext.ensembl.EnsemblCdna +........20 .........0 java.awt.FlowLayout +........18 .......143 javax.swing.JRadioButtonMenuItem +........18 .........3 java.util.Formatter.Flags +........18 .........1 java.awt.event.InvocationEvent +........18 .........0 java.awt.event.ItemEvent +........18 .........0 java.awt.BorderLayout +........16 .........0 jalview.datamodel.features.FeatureAttributes.AttributeData +........15 ........11 javax.swing.JPanel +........15 .........1 javax.swing.JComponent$2 +........14 .......406 jalview.datamodel.Alignment +........14 .........7 jalview.datamodel.HiddenColumns +........14 .........1 jalview.gui.ColourMenuHelper$3 +........14 .........0 java.util.LinkedList.ListItr +........14 .........0 jalview.schemes.JalviewColourScheme +........14 .........0 jalview.datamodel.HiddenSequences +........13 .........2 jalview.util.ReverseListIterator +........13 .........1 java.util.LinkedHashMap +........12 .........1 java.awt.AlphaComposite +........11 .........0 jalview.jbgui.GAlignFrame$1 +........10 .........0 java.util.BitSet +........10 .........0 java.awt.geom.Rectangle2D.Float +........10 .........0 java.awt.Color[] +.........9 .........1 java.util.LinkedHashMap.LinkedEntrySet +.........9 .........1 java.util.LinkedHashMap.LinkedEntryIterator +.........8 .........5 java.util.Formatter.FormatSpecifier +.........8 .........0 java.util.Formatter.FixedString +.........8 .........0 java.awt.Font +.........8 .........0 com.stevesoft.pat.Pthings +.........7 .........2 com.stevesoft.pat.Bracket +.........7 .........1 java.util.concurrent.ConcurrentHashMap.HashEntry +.........7 .........0 javax.swing.text.Segment +.........6 .........1 java.util.AbstractList.Itr +.........6 .........1 com.stevesoft.pat.SubMark +.........6 .........1 com.stevesoft.pat.OrMark +.........6 .........1 com.stevesoft.pat.FastMulti +.........6 .........0 swingjs.JSFontMetrics +.........6 .........0 javax.swing.SizeRequirements[] +.........6 .........0 javax.swing.DefaultBoundedRangeModel +.........6 .........0 java.util.Formatter.FormatString[] +.........6 .........0 jalview.datamodel.Range +.........6 .........0 com.stevesoft.pat.Range +.........5 .........1 swingjs.JSGraphics2D +.........5 .........0 sun.java2d.StateTrackableDelegate +.........5 .........0 javax.swing.event.InternalFrameEvent +.........5 .........0 java.awt.RenderingHints +.........5 .........0 jalview.renderer.ResidueShader +.........5 .........0 Boolean +.........4 .........3 javax.swing.JLabel +.........4 .........3 jalview.analysis.AnnotationSorter +.........4 .........2 java.util.concurrent.ConcurrentHashMap +.........4 .........1 jalview.analysis.AnnotationSorter$2 +.........4 .........0 sun.java2d.StateTrackable.State +.........4 .........0 javax.swing.JScrollBar.ModelListener +.........4 .........0 java.util.concurrent.ConcurrentHashMap.Segment[] +.........4 .........0 java.awt.geom.RectIterator +.........4 .........0 java.awt.event.AdjustmentEvent +.........4 .........0 jalview.ext.ensembl.EnsemblSeqProxy.EnsemblSeqType +.........4 .........0 jalview.analysis.AnnotationSorter$3 +.........4 .........0 jalview.analysis.AnnotationSorter$1 +.........4 .........0 com.stevesoft.pat.End +.........4 ........-1 jalview.datamodel.Annotation[] +.........3 ........46 java.awt.image.BufferedImage +.........3 .........4 java.awt.image.DataBufferInt +.........3 .........3 java.awt.image.DirectColorModel +.........3 .........1 java.awt.GridLayout +.........3 .........1 jalview.datamodel.StartRegionIterator +.........3 .........0 swingjs.JSToolkit$1 +.........3 .........0 sun.font.FontDesignMetrics.KeyReference +.........3 .........0 sun.font.FontDesignMetrics +.........3 .........0 javax.swing.ButtonGroup +.........3 .........0 java.util.regex.Matcher +.........3 .........0 java.util.Collections.SynchronizedSet +.........3 .........0 java.awt.image.SinglePixelPackedSampleModel +.........3 .........0 jalview.schemes.NucleotideColourScheme +.........3 .........0 jalview.renderer.ScaleRenderer +.........3 .........0 jalview.gui.AnnotationPanel.DragMode +.........3 .........0 jalview.datamodel.features.FeatureAttributes.Datatype +.........3 .........0 jalview.datamodel.VisibleContigsIterator +.........3 .........0 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder +.........2 .......190 javax.swing.JScrollBar +.........2 ........16 javax.swing.JScrollPane.ScrollBar +.........2 ........13 com.stevesoft.pat.Regex +.........2 ........10 javax.swing.JProgressBar +.........2 .........2 java.awt.Container +.........2 .........1 java.util.Hashtable.KeySet +.........2 .........1 java.lang.IndexOutOfBoundsException +.........2 .........1 java.awt.geom.Path2D.Float.CopyIterator +.........2 .........1 java.awt.geom.Path2D.Float +.........2 .........0 javax.swing.text.AbstractDocument.DefaultDocumentEvent +.........2 .........0 javax.swing.event.UndoableEditEvent +.........2 .........0 javax.swing.border.LineBorder +.........2 .........0 javax.swing.JProgressBar.ModelListener +.........2 .........0 java.util.LinkedHashMap.LinkedValues +.........2 .........0 java.util.LinkedHashMap.LinkedValueIterator +.........2 .........0 java.util.IdentityHashMap.KeyIterator +.........2 .........0 java.util.Collections.SynchronizedCollection +.........2 .........0 java.util.Collections.SingletonList +.........2 .........0 java.util.Collections$1 +.........2 .........0 java.util.ArrayDeque +.........2 .........0 java.lang.Thread +.........2 .........0 java.lang.StackTraceElement[] +.........2 .........0 java.awt.event.ActionEvent +.........2 .........0 jalview.util.IntRangeComparator +.........2 .........0 jalview.io.SequenceAnnotationReport +.........2 .........0 jalview.gui.AlignmentPanel[] +.........2 .........0 jalview.ext.ensembl.EnsemblSequenceFetcher.EnsemblFeatureType[] +.........2 .........0 jalview.ext.ensembl.EnsemblLookup +.........2 .........0 jalview.datamodel.features.RangeComparator +.........2 .........0 jalview.datamodel.SearchResults +.........2 .........0 jalview.datamodel.AlignmentAnnotation[] +.........2 .........0 jalview.datamodel.AlignmentAnnotation +.........2 .........0 jalview.controller.AlignViewController +.........2 .........0 com.stevesoft.pat.patInf +.........2 .........0 com.stevesoft.pat.Rthings +.........2 .........0 com.stevesoft.pat.Or +.........2 .........0 com.stevesoft.pat.NullPattern +.........1 .....11161 jalview.gui.AlignFrame +.........1 .......561 jalview.gui.AlignViewport +.........1 .......441 jalview.gui.AlignmentPanel +.........1 ........65 jalview.schemes.ColourSchemes +.........1 ........57 jalview.gui.SeqPanel +.........1 ........33 jalview.gui.SeqCanvas +.........1 ........19 javax.swing.JScrollPane +.........1 ........11 javax.swing.JTabbedPane +.........1 ........11 jalview.io.FileFormats +.........1 .........9 jalview.gui.FeatureRenderer +.........1 .........8 javax.swing.JRootPane +.........1 .........8 javax.swing.JInternalFrame.JDesktopIcon +.........1 .........8 jalview.gui.IdPanel +.........1 .........7 jalview.gui.AnnotationPanel +.........1 .........6 jalview.datamodel.ColumnSelection.IntList +.........1 .........6 jalview.datamodel.ColumnSelection +.........1 .........5 javax.swing.JToolTip +.........1 .........5 jalview.jbgui.GAlignFrame$79 +.........1 .........4 jalview.io.gff.SequenceOntologyLite +.........1 .........3 sun.awt.image.SunWritableRaster$1 +.........1 .........3 jalview.jbgui.GAlignFrame$72 +.........1 .........3 jalview.gui.ViewSelectionMenu +.........1 .........2 javax.swing.text.GapContent.RemoveUndo +.........1 .........2 javax.swing.JLayeredPane +.........1 .........2 jalview.util.LinkedIdentityHashSet$1 +.........1 .........2 jalview.jbgui.GAlignFrame$83 +.........1 .........2 jalview.gui.SequenceRenderer +.........1 .........2 jalview.gui.IdCanvas +.........1 .........2 jalview.ext.ensembl.EnsemblLookup$1 +.........1 .........1 swingjs.JSKeyEvent +.........1 .........1 javax.swing.JViewport +.........1 .........1 javax.swing.JMenuBar +.........1 .........1 java.util.concurrent.locks.ReentrantReadWriteLock.ReadLock +.........1 .........1 java.util.concurrent.locks.ReentrantReadWriteLock +.........1 .........1 jalview.viewmodel.seqfeatures.FeaturesDisplayed +.........1 .........1 jalview.jbgui.GAlignFrame$99 +.........1 .........1 jalview.jbgui.GAlignFrame$8 +.........1 .........1 jalview.jbgui.GAlignFrame$59 +.........1 .........1 jalview.jbgui.GAlignFrame$57 +.........1 .........1 jalview.jbgui.GAlignFrame$54 +.........1 .........1 jalview.jbgui.GAlignFrame$50 +.........1 .........1 jalview.jbgui.GAlignFrame$49 +.........1 .........1 jalview.jbgui.GAlignFrame$46 +.........1 .........1 jalview.jbgui.GAlignFrame$41 +.........1 .........1 jalview.jbgui.GAlignFrame$40 +.........1 .........1 jalview.jbgui.GAlignFrame$29 +.........1 .........1 jalview.jbgui.GAlignFrame$23 +.........1 .........1 jalview.jbgui.GAlignFrame$21 +.........1 .........1 jalview.jbgui.GAlignFrame$14 +.........1 .........1 jalview.jbgui.GAlignFrame$13 +.........1 .........1 jalview.jbgui.GAlignFrame$116 +.........1 .........1 jalview.jbgui.GAlignFrame$102 +.........1 .........1 jalview.io.SequenceAnnotationReport$1 +.........1 .........1 jalview.io.FileFormat$3 +.........1 .........1 jalview.io.FileFormat$13 +.........1 .........1 jalview.gui.ScalePanel +.........1 .........1 jalview.gui.ProgressBar +.........1 .........1 jalview.gui.IdwidthAdjuster +.........1 .........1 jalview.gui.ColourMenuHelper$1 +.........1 .........1 jalview.gui.AnnotationLabels +.........1 .........1 jalview.gui.AlignFrame$3 +.........1 .........1 jalview.datamodel.features.FeatureAttributes$1 +.........1 .........1 jalview.datamodel.features.FeatureAttributes +.........1 .........0 swingjs.plaf.Resizer +.........1 .........0 swingjs.plaf.LazyActionMap +.........1 .........0 swingjs.plaf.JSTabbedPaneUI.TabbedPaneLayout +.........1 .........0 swingjs.plaf.JSTabbedPaneUI.Handler +.........1 .........0 swingjs.plaf.JSScrollPaneUI.Handler +.........1 .........0 swingjs.plaf.JSMenuBarUI.Handler +.........1 .........0 swingjs.plaf.JSInternalFrameUI.Handler +.........1 .........0 swingjs.plaf.DefaultMenuLayout +.........1 .........0 swingjs.JSMouse +.........1 .........0 swingjs.JSFrameViewer +.........1 .........0 sun.java2d.StateTrackable.State[] +.........1 .........0 javax.swing.text.GapContent.UndoPosRef +.........1 .........0 javax.swing.text.GapContent.InsertUndo +.........1 .........0 javax.swing.plaf.basic.BasicBorders.MarginBorder +.........1 .........0 javax.swing.ScrollPaneLayout.UIResource +.........1 .........0 javax.swing.JViewport.ViewListener +.........1 .........0 javax.swing.JTabbedPane.ModelListener +.........1 .........0 javax.swing.JRootPane.RootLayout +.........1 .........0 javax.swing.JRootPane$1 +.........1 .........0 javax.swing.JComponent.IntVector +.........1 .........0 javajs.util.AjaxURLStreamHandler +.........1 .........0 javajs.api.JSFunction[] +.........1 .........0 java.util.concurrent.locks.ReentrantReadWriteLock.WriteLock +.........1 .........0 java.util.concurrent.ConcurrentHashMap.KeySet +.........1 .........0 java.util.concurrent.ConcurrentHashMap.KeyIterator +.........1 .........0 java.util.LinkedHashMap.LinkedKeySet +.........1 .........0 java.util.LinkedHashMap.LinkedKeyIterator +.........1 .........0 java.util.Hashtable.ValueCollection +.........1 .........0 java.util.Hashtable.EntrySet +.........1 .........0 java.util.Collections.UnmodifiableRandomAccessList +.........1 .........0 java.util.Collections.SynchronizedMap +.........1 .........0 java.util.Collections.EmptyIterator +.........1 .........0 java.util.Collections.EmptyEnumeration +.........1 .........0 java.lang.Thread[] +.........1 .........0 java.awt.event.WindowEvent +.........1 .........0 java.awt.event.FocusEvent +.........1 .........0 java.awt.dnd.DropTargetContext +.........1 .........0 java.awt.dnd.DropTarget +.........1 .........0 java.awt.color.ColorSpace +.........1 .........0 java.awt.Rectangle[] +.........1 .........0 java.awt.LightweightDispatcher +.........1 .........0 java.awt.EventQueueItem[] +.........1 .........0 jalview.workers.ConsensusThread +.........1 .........0 jalview.workers.AlignCalcManager +.........1 .........0 jalview.viewmodel.styles.ViewStyle +.........1 .........0 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jalview.gui.AlignFrame$1 +.........1 .........0 jalview.ext.ensembl.EnsemblSeqProxy.EnsemblSeqType[] +.........1 .........0 jalview.ext.ensembl.EnsemblGene$1$2 +.........1 .........0 jalview.ext.ensembl.EnsemblGene$1$1 +.........1 .........0 jalview.ext.ensembl.EnsemblGene$1 +.........1 .........0 jalview.ext.ensembl.EnsemblFeatures +.........1 .........0 jalview.datamodel.features.SequenceFeatures$2 +.........1 .........0 jalview.datamodel.features.SequenceFeatures$1 +.........1 .........0 jalview.datamodel.features.FeatureAttributes.Datatype[] +.........1 .........0 jalview.datamodel.Profiles +.........1 .........0 jalview.datamodel.ProfileI[] +.........1 .........0 jalview.analysis.CrossRef +.........1 .........0 jalview.analysis.CodonComparator +.........1 .........0 jalview.analysis.AnnotationSorter.SequenceAnnotationOrder[] +.........1 ........-1 jalview.schemes.Consensus[] +...5994529 ....111547 \ No newline at end of file diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip index 3ef9b4a..7079c67 100644 Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ diff --git a/swingjs/timestamp b/swingjs/timestamp index ce0a890..4f24039 100644 --- a/swingjs/timestamp +++ b/swingjs/timestamp @@ -1 +1 @@ -20190128204111 +20190129013326 diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip index 3ef9b4a..7079c67 100644 Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp index ce0a890..4f24039 100644 --- a/swingjs/ver/3.2.4/timestamp +++ b/swingjs/ver/3.2.4/timestamp @@ -1 +1 @@ -20190128204111 +20190129013326