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Merge branch 'JAL-1226' into Release_2_8_1_Branch_i18n

Merge branch 'JAL-1226' into Release_2_8_1_Branch

fix for JAL-1226

Merge branch 'JAL-686' into Release_2_8_1_Branch_i18n

Merge branch 'JAL-686' into develop

Merge branch 'JAL-686' into Release_2_8_1_Branch

JAL-1457 refactoring to explore why '-' appear in annotation rows (see AlignmentAnnotation.padGaps)

fix for JAL-686 - don't trim spaces before creating annotation

inprogress

    • -115
    • +131
    /forester/java/src/org/forester/msa/MsaCompactor.java
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n

Merge branch 'JAL-1454_patch' into develop

Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch

JAL-1355 typo in key

Merge branch 'JAL-1454_patch' into Release_2_8_1_Branch

JAL-1454 catch exceptions during calculation and report any warnings in the PCA 'Output values...' dump.

JAL-1454 increase max for tqli iterations and throw exception rather than call System.exit()

kind of pointless addition

inprogress

inprogress

Merge branch 'JAL-1364_patch' into develop

Merge branch 'JAL-1364_patch' into Release_2_8_1_Branch

patch for JAL-1449 - continuance of JAL-1364 - check bounds of gapMap - not the VIENNA results

    • -2
    • +6
    /src/jalview/ws/jws2/RNAalifoldClient.java
Merge branch 'Release_2_8_1_Branch' into Release_2_8_1_Branch_i18n

Merge branch 'pathc_JAL-1354' into develop

Merge branch 'pathc_JAL-1354' into Release_2_8_1_Branch

JAL-1448 reinstate non-locale sensitive code for reading/writing last read date from RSS and Jalview preferences

JAL-1354 use real var-args method signature to avoid ambiguity

JAL-1354 quoted format strings are not substituted

inprogress