Jan Engelhardt

Merge branch '2_5_1_rna_merge' of https://source.jalview.org/git/jalview into 2_5_1_rna_merge

Sequence name in VARNA windows was not correct (always contained "consensus-"). The addition of the prefix is therefore moved from AppVarna to PopUpMenu.

Change-Id: I7e0cd46bce9eee07726678742e5f8046f7f528af

Including of VARNAv-3.9;

Change-Id: Ib55f047ae763999c7db2b601105b6655132ee171

JAL-913; Extending documentation; VARNA help;

Change-Id: If1deae2cf040ac9a28ab770019a0e3040f74daeb

    • -0
    • +6
    /help/html/calculations/consensus.html
    • -0
    • +44
    /help/html/calculations/structureconsensus.html
    • -0
    • +74
    /help/html/features/varna.html
JAL-913; Documentation of RNA Structure Conservation

Change-Id: I695f08d01e4feba87b5c5f15981896f7ee484dd4

    • -0
    • +1
    /.externalToolBuilders/Jalview Release indices [Builder].launch
    • -0
    • +28
    /help/html/calculations/structureconservation.html
JAL-842; Text element containing the structure is not visible anymore in VARNA;

Change-Id: I589055fe74542eae28bc7a5ff47180eaee83c5a3

JAL-891; Tooltips for Structure logos implemented;

Change-Id: I8601aa5b9b9c50e9c1a7b8f6f39dd6f6e358cf6a

JAL-878; Structures associated to a sequence are available via Popupmenu;

Change-Id: I20050a77bf494782893d6383f3d2e901cae7d3f1

    • -136
    • +168
    /src/jalview/gui/PopupMenu.java
JAL-891; Labeling of structure conservation is improved a bit. Brackets instead of 'H'.

Change-Id: I220e86f21e2ff539ab5828bba4c0d07d76777422

JAL-891; Sorting of Structure logo implemented; bug that caused exception after editing a structure solved (sequences have different lengths after editing);

Change-Id: If2cb0ea0c683dc99a5df7002a4f9907283ce27cb

JAL-885; hasRNAStructure method was introduced to AlignmentI and Alignment; determines if Alignment contains an RNA structure; Structure conservation row is just added if yes;

Change-Id: I6fa20f14e54cd656c65f82bc6b68f84d1d6f2c64

    • -0
    • +10
    /src/jalview/datamodel/Alignment.java
    • -8
    • +17
    /src/jalview/datamodel/AlignmentI.java
JAL-885; Structure conservation row is just added if alignment isNucleotide(); StructureFrequency.java cleaned;

Change-Id: Ic86908cbea0791e7174b440cc4c7e7b12b978927

    • -7
    • +12
    /src/jalview/gui/AlignViewport.java
JAL-891; base-pair logos can now be activated for structure conservation row;

Change-Id: Ib3450f328f901eaf12ea094c9c914322f8398a88

    • -208
    • +255
    /src/jalview/analysis/StructureFrequency.java
JAL-891; structure logo is adapted to two char's; Missing: calculate bp frequencies and include them in the draw-part;

Change-Id: Ie43edd7a074f6b219c808fa2519d2b88659f30e5

    • -83
    • +113
    /src/jalview/gui/AlignViewport.java
    • -133
    • +186
    /src/jalview/gui/AnnotationPanel.java
JAL-891; sequence logos are available on structure conservation row now; has to be adopted to base pair interaction;

Change-Id: I86cf329d794d6ff78cb4bb4c5248cadcc34b2681

    • -1
    • +28
    /src/jalview/gui/AnnotationPanel.java
JAL-885; Multi-helix bug is solved; One should think about a more efficient solution; either by creating a Hashtable of pairs in StructureFrequency or directly in a RNA class;

Change-Id: I7bd21eb4d952f22579c786f3d78395949fa046d0

JAL-885; StructureConservation row is displayed at the bottom of the AlignmentPanel; StructureFrequency class was introduced and is called by thread in AlignViewport that is called by AlignFrame; everything is according to Conservation-Row

Change-Id: I3753bbb5678147cbc0c9d1d6bc1a4886b0551a59

    • -1
    • +0
    /src/jalview/analysis/AAFrequency.java
    • -8
    • +26
    /src/jalview/gui/AlignViewport.java
JAL-885; Implementation of StructureFrequency.java and according methods in AlignViewport.java; completeConsensus is still missing;

Change-Id: I3678fc75af84aa5a8974faed6b76f47c76a74638

    • -0
    • +1
    /src/jalview/analysis/AAFrequency.java
    • -1
    • +0
    /src/jalview/analysis/Conservation.java
    • -0
    • +488
    /src/jalview/analysis/StructureFrequency.java
    • -2
    • +129
    /src/jalview/gui/AlignViewport.java
some print statements to test things

Change-Id: I0730499d395e8f84b9cfd9ec2aaaa7283fc4b1fa

    • -1
    • +1
    /src/jalview/io/AppletFormatAdapter.java
JAL-882; VARNA crashed when non-standard gaps where in structure; the are now replaced with standard gaps before commiting to VARNA in AppVarna.java

Change-Id: I36b523fb7f1063dc2fa5924cb4569f15e0067df2

    • -9
    • +48
    /src/jalview/gui/AnnotationPanel.java
JAL-878; Additional structures with a 'GR' tag in StockholmFiles are associated their specific sequence.

Change-Id: I26913db05bef3983b63397304c97351f5361d61d

JAL-842; toy example to insert nucleotides in sequences in the AlignmentPanel;

Change-Id: I9901d08b1f06861c4d9b7795a4a935ac040d7b2b

    • -1
    • +20
    /src/jalview/commands/EditCommand.java
JAL-842; Implement transmitting of Jalview Sequence highlights to Varna

Change-Id: I8e1fbc375cdcec6cf36a46cdac56800740c42180

    • -1
    • +17
    /src/jalview/gui/AppVarnaBinding.java
    • -0
    • +27
    /src/jalview/structure/SecondaryStructureListener.java
JAL-842: some bugfixes;

Change-Id: Ia349eeb750da7b51673a76be805737e4356524e7

    • -11
    • +1
    /src/jalview/gui/AppVarnaBinding.java
JAL-842; Added the TextField to edit structure in VARNA

Change-Id: I93a90da2468c4c6b69570aac9741b286300b6430

    • -19
    • +24
    /src/jalview/gui/AppVarnaBinding.java
JAL-842; trimming single structures for single sequences added;

Change-Id: I041c71aafd0081875b948b9978c2411154033408

JAL-842; Give Varna frames name for window organizer; always display the consensus structure and the 'trimmed' structure for a sequence;

Change-Id: If4e9b054455de3c0f43967e27fb399df4c23b751

    • -25
    • +38
    /src/jalview/gui/AppVarnaBinding.java
Varna external frame bug solved

Change-Id: Ie60149059d664fb63d6bd99d748c1f34c1b01703

Reorganize the class structure, unfortunately breaks the VARNA-Frame

Change-Id: Ia3dde7af1beb73e9261e49e81afe3e8594c945bb

    • -1498
    • +2
    /src/jalview/ext/varna/JalviewVarnaBinding.java
    • -23
    • +224
    /src/jalview/gui/AppVarnaBinding.java
clean code

Change-Id: I43a5703ed1dee98dbad0b15226dbe21a87fb6ead

    • -3
    • +1
    /src/jalview/gui/AnnotationLabels.java