ongoign vamsas session debugging

updated to jalview 2.1 and begun ArchiveClient/VamsasClient/VamsasStore updates.

This commit was manufactured by cvs2svn to create branch 'VamJalview'.

Cherrypick from master 2006-09-07 11:39:36 UTC jimp 'added copy consensus sequence to consensus annotation popup menu':
    src/jalview/appletgui/Tooltip.java
    src/jalview/datamodel/.cvsignore
    src/jalview/datamodel/AlignmentView.java
    src/jalview/datamodel/CigarArray.java
    src/jalview/datamodel/CigarBase.java
    src/jalview/datamodel/CigarCigar.java
    src/jalview/datamodel/CigarSimple.java
    src/jalview/datamodel/ColumnSelection.java
    src/jalview/datamodel/DBRefSource.java
    src/jalview/datamodel/SeqCigar.java
    src/jalview/datamodel/UniprotProteinName.java
    src/jalview/gui/AnnotationExporter.java
    src/jalview/gui/DasSourceBrowser.java
    src/jalview/gui/Jalview2XML_V1.java
    src/jalview/io/AnnotationFile.java
    src/jalview/io/DBRefFetcher.java
    src/jalview/io/DasSequenceFeatureFetcher.java
    src/jalview/io/FeaturesFile.java
    src/jalview/io/JnetAnnotationMaker.java
    src/jalview/io/StockholmFile.java
    src/jalview/jbgui/GDasSourceBrowser.java
    src/jalview/schemabinding/version2/Alignment.java
    src/jalview/schemabinding/version2/AlignmentDescriptor.java
    src/jalview/schemabinding/version2/Annotation.java
    src/jalview/schemabinding/version2/AnnotationColours.java
    src/jalview/schemabinding/version2/AnnotationColoursDescriptor.java
    src/jalview/schemabinding/version2/AnnotationDescriptor.java
    src/jalview/schemabinding/version2/AnnotationElement.java
    src/jalview/schemabinding/version2/AnnotationElementDescriptor.java
    src/jalview/schemabinding/version2/Colour.java
    src/jalview/schemabinding/version2/ColourDescriptor.java
    src/jalview/schemabinding/version2/DBRef.java
    src/jalview/schemabinding/version2/DBRefDescriptor.java
    src/jalview/schemabinding/version2/Feature.java
    src/jalview/schemabinding/version2/FeatureDescriptor.java
    src/jalview/schemabinding/version2/FeatureSettings.java
    src/jalview/schemabinding/version2/FeatureSettingsDescriptor.java
    src/jalview/schemabinding/version2/Features.java
    src/jalview/schemabinding/version2/FeaturesDescriptor.java
    src/jalview/schemabinding/version2/HiddenColumns.java
    src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
    src/jalview/schemabinding/version2/JGroup.java
    src/jalview/schemabinding/version2/JGroupDescriptor.java
    src/jalview/schemabinding/version2/JSeq.java
    src/jalview/schemabinding/version2/JSeqDescriptor.java
    src/jalview/schemabinding/version2/JalviewModel.java
    src/jalview/schemabinding/version2/JalviewModelDescriptor.java
    src/jalview/schemabinding/version2/JalviewModelSequence.java
    src/jalview/schemabinding/version2/JalviewModelSequenceDescriptor.java
    src/jalview/schemabinding/version2/JalviewUserColours.java
    src/jalview/schemabinding/version2/JalviewUserColoursDescriptor.java
    src/jalview/schemabinding/version2/OtherData.java
    src/jalview/schemabinding/version2/OtherDataDescriptor.java
    src/jalview/schemabinding/version2/Pdbentry.java
    src/jalview/schemabinding/version2/PdbentryDescriptor.java
    src/jalview/schemabinding/version2/PdbentryItem.java
    src/jalview/schemabinding/version2/PdbentryItemDescriptor.java
    src/jalview/schemabinding/version2/Pdbids.java
    src/jalview/schemabinding/version2/PdbidsDescriptor.java
    src/jalview/schemabinding/version2/Property.java
    src/jalview/schemabinding/version2/PropertyDescriptor.java
    src/jalview/schemabinding/version2/Sequence.java
    src/jalview/schemabinding/version2/SequenceDescriptor.java
    src/jalview/schemabinding/version2/SequenceSet.java
    src/jalview/schemabinding/version2/SequenceSetDescriptor.java
    src/jalview/schemabinding/version2/SequenceType.java
    src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
    src/jalview/schemabinding/version2/Setting.java
    src/jalview/schemabinding/version2/SettingDescriptor.java
    src/jalview/schemabinding/version2/ThresholdLine.java
    src/jalview/schemabinding/version2/ThresholdLineDescriptor.java
    src/jalview/schemabinding/version2/Tree.java
    src/jalview/schemabinding/version2/TreeDescriptor.java
    src/jalview/schemabinding/version2/UserColourScheme.java
    src/jalview/schemabinding/version2/UserColourSchemeDescriptor.java
    src/jalview/schemabinding/version2/UserColours.java
    src/jalview/schemabinding/version2/UserColoursDescriptor.java
    src/jalview/schemabinding/version2/VAMSAS.java
    src/jalview/schemabinding/version2/VAMSASDescriptor.java
    src/jalview/schemabinding/version2/VamsasModel.java
    src/jalview/schemabinding/version2/VamsasModelDescriptor.java
    src/jalview/schemabinding/version2/Viewport.java
    src/jalview/schemabinding/version2/ViewportDescriptor.java
    src/jalview/util/ShiftList.java
    src/jalview/util/TableSorter.java
    src/jalview/ws/MsaWSThread.java
    src/jalview/ws/WSThread.java
    src/org/biojava/dasobert/das/DAS_FeatureRetrieve.java
    src/org/biojava/dasobert/das/DAS_Feature_Handler.java
    src/org/biojava/dasobert/das/FeatureThread.java
    src/org/biojava/dasobert/das2/Das2Capability.java
    src/org/biojava/dasobert/das2/Das2CapabilityImpl.java
    src/org/biojava/dasobert/das2/Das2Source.java
    src/org/biojava/dasobert/das2/Das2SourceImpl.java
    src/org/biojava/dasobert/das2/DasSourceConverter.java
    src/org/biojava/dasobert/das2/io/DAS2SourceHandler.java
    src/org/biojava/dasobert/das2/io/DasSourceReader.java
    src/org/biojava/dasobert/das2/io/DasSourceReaderImpl.java
    src/org/biojava/dasobert/dasregistry/Das1Source.java
    src/org/biojava/dasobert/dasregistry/Das2Validator.java
    src/org/biojava/dasobert/dasregistry/DasCoordSysComparator.java
    src/org/biojava/dasobert/dasregistry/DasCoordinateSystem.java
    src/org/biojava/dasobert/dasregistry/DasSource.java
    src/org/biojava/dasobert/dasregistry/DasSourceComparator.java
    src/org/biojava/dasobert/eventmodel/FeatureEvent.java
    src/org/biojava/dasobert/eventmodel/FeatureListener.java
    src/org/biojava/dasobert/eventmodel/ObjectListener.java
    src/org/biojava/dasobert/eventmodel/SequenceEvent.java
    src/org/biojava/dasobert/eventmodel/SequenceListener.java

part finished (still finishing the updateJalview method of VamsasDatastore)

preliminary notes on javliew sync with vamsas document

modified constructor for jalview.gui.VamsasClient

refactored VamsasClient to jalview.gui, and created Vamsas session menu.

basic VamsasSession gui bits.

Feature settings

Has its own featureRenderer

Group colours not used

Associated Data menu item

Cursor added

Typo

fr.transferSettings

FeatureSettings bug fixed

Feature added to group search results

Groups compatibility

No need to hava SSX as array

CursoMode added

Load data file added

Trim line

Features added to group Uniprot

Add check if sequence already exists

FeaturesGroup added to constructor

1 too many

Features added to group search results

-1 +1 check removed

1 too many in drawgraph

Annotation colour scheme added

Called from AnnotationColourChooser and Feature Settings

Annotation colours added to applet

ZSort no longer static

Has own featurerenderer

Rearranged text

Correct reference

typo

Reference added

added example jnlp to memory settings help

added link to example jnlp file

example jnlp file for users to edit and save locally

jnet method description correction.

Fix for Finn Drablos bug. Must use equals for comparing strings

historyItem.restore

HideSequences

getWidth and getHeight just once

-1 to drawGraphs

isVisible and hiddenboundary added

UserColors not used here

Hidden Rows

Reveal

Faster

Hide Sequences

Tooltip for hidden columns

Hidden column adjustments

Scrolls when editing

Gethidden sequences

HiddenSequence methods

getHiddenSequences

Keeps a record of hidden sequences

Allow loading from Zip files

Load tree

CandP takes AlignFrame, not applet

Fastpaint updates

Check endres when drawing graphs

Cut and paste may be inserted into Dialog frame

Fastest implementation so far

Extra argument false

Scroll implemented for applet editing

Selection Group rendering updated

Reduced arguments for speed

Can be used for user features

Add new feature from seqrch results

Feature rendering in groups

Out of bounds check

added description of alignment quality scores and separated
description of conservation calculation from the instructions for
colouring alignments by it.

methods for searching DBRef lists

fixes bug 0013013 but reveals lack of a 'features retrieved' flag that should be set when a sequence's uniprot record has been retrieved and all its sequence features have been added.

bug fix for 0013013

Sequences can have a description

Features may belong to a feature group

IdentifyFile should not be static

Can read from zip file

Blank space is white

Reveal All added

<= fastPaints hidden columns

Check for visibleGroup==null

IdentfyFile should not be static

RevealAllHiddenColumns

Allow for hidden columns

Able to read resources from Zip file

Blank space is white

PASTE is constant in AppletFormatAdapter

Pack resources in Zip file

fixed after refactoring of SequenceFeature[] seq.getSequenceFeatures

propagate SearchResult object use to MCView's highlighted residue renderer.

P1 changed to N1

Add Annotation to specific sequence

Cannot delete residues

Features now array