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Fetch Sequences...PDB - all tabs working
authorhansonr <hansonr@STO24954W.ad.stolaf.edu>
Tue, 29 Jan 2019 07:39:55 +0000 (01:39 -0600)
committerhansonr <hansonr@STO24954W.ad.stolaf.edu>
Tue, 29 Jan 2019 07:39:55 +0000 (01:39 -0600)
Could still be a problem with panels being moved to and from being
content panes.

optimization/full-profile-ENSG000000157764-to-display-chrome.txt [new file with mode: 0644] patch | blob
optimization/full-profile-ENSG000000157764-to-display-ff.txt [new file with mode: 0644] patch | blob
swingjs/SwingJS-site.zip patch | blob | history
swingjs/timestamp patch | blob | history
swingjs/ver/3.2.4/SwingJS-site.zip patch | blob | history
swingjs/ver/3.2.4/timestamp patch | blob | history

diff --git a/optimization/full-profile-ENSG000000157764-to-display-chrome.txt b/optimization/full-profile-ENSG000000157764-to-display-chrome.txt
new file mode 100644 (file)
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
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+.........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
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+.........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
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+.........2     .........0              java.util.LinkedHashMap.LinkedValueIterator
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+.........1     ........26              jalview.gui.IdPanel
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+.........1     .........7              sun.awt.image.SunWritableRaster$1
+.........1     .........7              jalview.gui.AnnotationPanel
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+.........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[]
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+.........1     .........0              jalview.renderer.ResidueColourFinder
+.........1     .........0              jalview.renderer.AnnotationRenderer
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+.........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
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+.........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     .........0              jalview.jbgui.GAlignFrame$83
+.........1     .........0              jalview.jbgui.GAlignFrame$82
+.........1     .........0              jalview.jbgui.GAlignFrame$81
+.........1     .........0              jalview.jbgui.GAlignFrame$80
+.........1     .........0              jalview.jbgui.GAlignFrame$8
+.........1     .........0              jalview.jbgui.GAlignFrame$79
+.........1     .........0              jalview.jbgui.GAlignFrame$78
+.........1     .........0              jalview.jbgui.GAlignFrame$77
+.........1     .........0              jalview.jbgui.GAlignFrame$76
+.........1     .........0              jalview.jbgui.GAlignFrame$75
+.........1     .........0              jalview.jbgui.GAlignFrame$74
+.........1     .........0              jalview.jbgui.GAlignFrame$73
+.........1     .........0              jalview.jbgui.GAlignFrame$71
+.........1     .........0              jalview.jbgui.GAlignFrame$70
+.........1     .........0              jalview.jbgui.GAlignFrame$7
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+.........1     .........0              jalview.jbgui.GAlignFrame$68
+.........1     .........0              jalview.jbgui.GAlignFrame$67
+.........1     .........0              jalview.jbgui.GAlignFrame$66
+.........1     .........0              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
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+.........1     .........0              jalview.jbgui.GAlignFrame$51
+.........1     .........0              jalview.jbgui.GAlignFrame$50
+.........1     .........0              jalview.jbgui.GAlignFrame$5
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+.........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
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+.........1     .........0              jalview.jbgui.GAlignFrame$41
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+.........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$1
+.........1     .........0              jalview.datamodel.features.FeatureAttributes
+.........1     .........0              jalview.datamodel.Profiles
+.........1     .........0              jalview.analysis.CrossRef
+.........1     .........0              jalview.analysis.CodonComparator
+.........1     .........0              jalview.analysis.AnnotationSorter.SequenceAnnotationOrder[]
+.........1     ........-1              jalview.datamodel.ProfileI[]
+...5993224     .....61225      
\ No newline at end of file
diff --git a/optimization/full-profile-ENSG000000157764-to-display-ff.txt b/optimization/full-profile-ENSG000000157764-to-display-ff.txt
new file mode 100644 (file)
index 0000000..0d48473
--- /dev/null
+++ b/optimization/full-profile-ENSG000000157764-to-display-ff.txt
@@ -0,0 +1,514 @@
+"run  Clazz.startProfiling() first
+
+ Total new objects: 3208398
+
+count          exec(ms)
+--------       --------        ------------------------------
+...2100232     ....-40921              undefined[]
+....504006     .....12402              java.lang.StringBuilder
+....436605     ......3414              java.util.HashMap.Node
+....411205     ......2841              jalview.datamodel.Annotation
+....232907     ......1122              Float
+....215619     ......2440              jalview.datamodel.features.FeatureStore$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
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+........22     ........21              javax.swing.JPopupMenu
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+........22     .........2              java.util.TimSort
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\ No newline at end of file
diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip
index 3ef9b4a..7079c67 100644 (file)
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 (file)
--- 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 (file)
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 (file)
--- a/swingjs/ver/3.2.4/timestamp
+++ b/swingjs/ver/3.2.4/timestamp
@@ -1 +1 @@
-20190128204111 
+20190129013326