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formatting and cleanup
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@andersla
andersla committed Oct 28, 2017
1 parent 0b2a98e commit 68a7586
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Showing 5 changed files with 21 additions and 45 deletions.
2 changes: 2 additions & 0 deletions AliView.l4j.ini
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@@ -1 +1,3 @@
-Xmx1024m


1 change: 0 additions & 1 deletion aliview-windows/install.readme.txt
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Expand Up @@ -6,7 +6,6 @@ Download and run AliView-Setup.exe
alignment type files.



----*** ALTERNATIVE ***----
In directory "without_installer_version" is the program provided either as an .exe-file or a jar-file:

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44 changes: 10 additions & 34 deletions gencodes.txt
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@@ -1,21 +1,19 @@

public static final GeneticCode GC5 = new GeneticCode(6,"The Ciliate, Dasycladacean and Hexamita Nuclear Code", "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG");
public static final GeneticCode GC5 = new GeneticCode(6,"The Ciliate, Dasycladacean and Hexamita Nuclear Code",

"FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG");
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG




9. The Echinoderm and Flatworm Mitochondrial Code (transl_table=9)

AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG




10. The Euplotid Nuclear Code (transl_table=10)

AAs = FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Expand All @@ -24,7 +22,6 @@ public static final GeneticCode GC5 = new GeneticCode(6,"The Ciliate, Dasyclada
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG


11. The Bacterial, Archaeal and Plant Plastid Code (transl_table=11)

AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Expand All @@ -33,9 +30,6 @@ public static final GeneticCode GC5 = new GeneticCode(6,"The Ciliate, Dasyclada
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format


12. The Alternative Yeast Nuclear Code (transl_table=12)

AAs = FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Expand All @@ -44,27 +38,22 @@ Click here to change format
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG



13. The Ascidian Mitochondrial Code (transl_table=13)

AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
Starts = ---M------------------------------MM---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG



14. The Alternative Flatworm Mitochondrial Code (transl_table=14)

AAs = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG




15. Blepharisma Nuclear Code (transl_table=15)

AAs = FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Expand All @@ -73,36 +62,30 @@ Click here to change format
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG




16. Chlorophycean Mitochondrial Code (transl_table=16)

AAs = FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG



21. Trematode Mitochondrial Code (transl_table=21)

AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG



21. Trematode Mitochondrial Code (transl_table=21)

AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M---------------M------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG



23. Thraustochytrium Mitochondrial Code (transl_table=23)

AAs = FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Expand All @@ -111,9 +94,6 @@ Click here to change format
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format


24. Pterobranchia mitochondrial code (transl_table=24)

AAs = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG
Expand All @@ -122,9 +102,6 @@ Click here to change format
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format


25. Candidate Division SR1 and Gracilibacteria Code (transl_table=25)

AAs = FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Expand All @@ -133,5 +110,4 @@ Click here to change format
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Click here to change format

Binary file added icon_images/alignment_ico_64x64_v3_copy.png
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19 changes: 9 additions & 10 deletions innosetupfil_for_Aliview_win.iss
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Expand Up @@ -41,23 +41,23 @@ Name: "quicklaunchicon"; Description: "{cm:CreateQuickLaunchIcon}"; GroupDescrip

[Registry]
Root: HKCR; Subkey: ".nex"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_nex"; Flags: uninsdeletevalue; Tasks: nexAssociation
Root: HKCR; Subkey: ".nexus"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_nex"; Flags: uninsdeletevalue; Tasks: nexAssociation
Root: HKCR; Subkey: ".nexus"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_nex"; Flags: uninsdeletevalue; Tasks: nexAssociation
Root: HKCR; Subkey: "{#MyAppName}_nex"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}"; Flags: uninsdeletekey; Tasks: nexAssociation
Root: HKCR; Subkey: "{#MyAppName}_nex\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppName}"" ""%1"""
Root: HKCR; Subkey: ".phy"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_phy"; Flags: uninsdeletevalue; Tasks: phyAssociation
Root: HKCR; Subkey: ".phylip"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_phy"; Flags: uninsdeletevalue; Tasks: phyAssociation
Root: HKCR; Subkey: ".phy"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_phy"; Flags: uninsdeletevalue; Tasks: phyAssociation
Root: HKCR; Subkey: ".phylip"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_phy"; Flags: uninsdeletevalue; Tasks: phyAssociation
Root: HKCR; Subkey: "{#MyAppName}_phy"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}"; Flags: uninsdeletekey; Tasks: phyAssociation
Root: HKCR; Subkey: "{#MyAppName}_phy\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppName}"" ""%1"""
Root: HKCR; Subkey: ".fas"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletevalue; Tasks: fasAssociation
Root: HKCR; Subkey: ".fa"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletevalue; Tasks: fasAssociation
Root: HKCR; Subkey: ".fasta"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletevalue; Tasks: fasAssociation
Root: HKCR; Subkey: ".fas"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletevalue; Tasks: fasAssociation
Root: HKCR; Subkey: ".fa"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletevalue; Tasks: fasAssociation
Root: HKCR; Subkey: ".fasta"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletevalue; Tasks: fasAssociation
Root: HKCR; Subkey: "{#MyAppName}_fas"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_fas"; Flags: uninsdeletekey; Tasks: fasAssociation
Root: HKCR; Subkey: "{#MyAppName}_fas\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppName}"" ""%1"""
Root: HKCR; Subkey: ".clustal"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_clustal"; Flags: uninsdeletevalue; Tasks: clustalAssociation
Root: HKCR; Subkey: ".aln"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_clustal"; Flags: uninsdeletevalue; Tasks: clustalAssociation
Root: HKCR; Subkey: ".clustal"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_clustal"; Flags: uninsdeletevalue; Tasks: clustalAssociation
Root: HKCR; Subkey: ".aln"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_clustal"; Flags: uninsdeletevalue; Tasks: clustalAssociation
Root: HKCR; Subkey: "{#MyAppName}_clustal"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}"; Flags: uninsdeletekey; Tasks: clustalAssociation
Root: HKCR; Subkey: "{#MyAppName}_clustal\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppName}"" ""%1"""
Root: HKCR; Subkey: ".msf"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_msf"; Flags: uninsdeletevalue; Tasks: msfAssociation
Root: HKCR; Subkey: ".msf"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}_msf"; Flags: uninsdeletevalue; Tasks: msfAssociation
Root: HKCR; Subkey: "{#MyAppName}_msf"; ValueType: string; ValueName: ""; ValueData: "{#MyAppName}"; Flags: uninsdeletekey; Tasks: msfAssociation
Root: HKCR; Subkey: "{#MyAppName}_msf\shell\open\command"; ValueType: string; ValueName: ""; ValueData: """{app}\{#MyAppName}"" ""%1"""

Expand All @@ -73,4 +73,3 @@ Name: "{userappdata}\Microsoft\Internet Explorer\Quick Launch\{#MyAppName}"; Fil

[Run]
Filename: "{app}\{#MyAppExeName}"; Description: "{cm:LaunchProgram,{#StringChange(MyAppName, '&', '&&')}}"; Flags: nowait postinstall skipifsilent

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