Developing Jalview

know · CABIOS

javaws http://www.jalview.org/webstart/jalview.jnlp -open
- yourFileName
java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] 
javaws http://www.jalview.org/webstart/jalview.jnlp -open
+ yourFileName
java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] 
@[a-zA-Z]+
@mylink
 java Preferences
 
/lib
<INST_DIR>
/lib/ext
/jdev/lib/ext
<INST_DIR&g
 into the /jars directory of your jEdit distribution.
 jEdit will then need to be restarted before Jalopy begins working.
 
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9.3. License  Home  10.2. Integration
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net

diff --git a/utils/jalopy/docs/plugin-netbeans-integration.html b/utils/jalopy/docs/plugin-netbeans-integration.html
index e79f6a6..d242ca0 100755
--- a/utils/jalopy/docs/plugin-netbeans-integration.html
+++ b/utils/jalopy/docs/plugin-netbeans-integration.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -43,4 +60,4 @@ If it happens that a file has an open editor view, this view will be updated,
 not the actual file. You have to save the view first to see the physical file
 updated.
 
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Chapter 11. NetBeans/Sun ONE Studio module  Home  11.3. License
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/plugin-netbeans-license.html b/utils/jalopy/docs/plugin-netbeans-license.html
index cff0efe..431270a 100755
--- a/utils/jalopy/docs/plugin-netbeans-license.html
+++ b/utils/jalopy/docs/plugin-netbeans-license.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -23,4 +40,4 @@ for more information.
 See Appendix B, The Jalopy BSD License for the Jalopy license
 and refer to Appendix A, Library Dependencies for the license terms of the accompanying 3rd party libraries.
 
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11.2. Integration  Home  Appendix A. Library Dependencies
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/plugin-netbeans.html b/utils/jalopy/docs/plugin-netbeans.html
index ff1bca4..01a46df 100755
--- a/utils/jalopy/docs/plugin-netbeans.html
+++ b/utils/jalopy/docs/plugin-netbeans.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -56,4 +73,4 @@ Downloaded Modules (.nbm Files)', select the .nbm cont
 in <INST_DIR>/lib and
 proceed through all steps of the wizard as outlined.
 
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10.3. License  Home  11.2. Integration
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/plugins.html b/utils/jalopy/docs/plugins.html
index a6e716d..619c698 100755
--- a/utils/jalopy/docs/plugins.html
+++ b/utils/jalopy/docs/plugins.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -20,4 +37,4 @@ to get more information.
 
Ant 1.4 or above
Console (Command line tool)
Eclipse 3.0 or above
JBuilder 5.0 or above
JDeveloper 10g
jEdit 4.1pre1 or above
NetBeans 3.3 or above

 More to come!
 
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-            Copyright © 2001-2002, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2002, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/printer.html b/utils/jalopy/docs/printer.html
index 804a409..523af86 100755
--- a/utils/jalopy/docs/printer.html
+++ b/utils/jalopy/docs/printer.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -197,4 +214,4 @@ if (in != null)
     catch (IOException ignored) {}
 }
 
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4.2. Projects  Home  4.3.2. White Space
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/project.html b/utils/jalopy/docs/project.html
index fc4a9ca..d5dda34 100755
--- a/utils/jalopy/docs/project.html
+++ b/utils/jalopy/docs/project.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -37,4 +54,4 @@ avoid characters that your platform does not allow to be used in file paths.
 is not active. The default project cannot be removed.
Activate
Activates the selected project. The stored settings will be loaded and the
 configuration dialog updates accordingly.

 
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Chapter 4. Settings  Home  4.3. Printer
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/separation.html b/utils/jalopy/docs/separation.html
index 29d2cb3..1d6776d 100755
--- a/utils/jalopy/docs/separation.html
+++ b/utils/jalopy/docs/separation.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -283,4 +300,4 @@ Add separator comments for inner classes
 The insertion of separator comments for inner classes/interfaces may lead to
 confusion, therefore you can control it here separately.
 
4.3.5.3.2. Descriptions
Lets you define the description text for each of the different class elements.
4.3.5.3.3. Fill character
Lets you define the fill character for the comments.
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4.3.4. Wrapping  Home  4.3.6. Comments
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/settings.html b/utils/jalopy/docs/settings.html
index ff38d85..edc24ff 100755
--- a/utils/jalopy/docs/settings.html
+++ b/utils/jalopy/docs/settings.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -70,4 +87,4 @@ However if the backup directory setting is left untouched, the directory is
 stored relative to the Jalopy settings directory. This way you can savely
 share your code convention across different systems and platforms.
 
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Chapter 3. Usage  Home  4.2. Projects
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/sorting.html b/utils/jalopy/docs/sorting.html
index f1c46d7..8dc5575 100755
--- a/utils/jalopy/docs/sorting.html
+++ b/utils/jalopy/docs/sorting.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -73,4 +90,4 @@ Lets you specify the order in which the individual modifiers should appear.
 Select an entry and use the Up and Down
 buttons to move it to the desired location.
 
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4.3.11. Footer  Home  4.3.13. Misc
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/usage.html b/utils/jalopy/docs/usage.html
index 7779394..e823adc 100755
--- a/utils/jalopy/docs/usage.html
+++ b/utils/jalopy/docs/usage.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -18,4 +35,4 @@
                     This page generated: June 8 2004Chapter 3. Usage
Prev  Part I. Jalopy core  Next
Chapter 3. Usage
Usage depends on the distribution you received. Please refer to the
 individual Plug-in chapters in Part II, “Plug-ins” for details.
 
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Chapter 2. Building  Home  Chapter 4. Settings
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/whitespace.html b/utils/jalopy/docs/whitespace.html
index 9d2348e..e5ae4b1 100755
--- a/utils/jalopy/docs/whitespace.html
+++ b/utils/jalopy/docs/whitespace.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -222,4 +239,4 @@ int line = ((JavaAST)
 
 int line = (( JavaAST )node).getStartLine();
 
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4.3. Printer  Home  4.3.3. Indentation
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/docs/wrapping.html b/utils/jalopy/docs/wrapping.html
index 54a037d..e2352b6 100755
--- a/utils/jalopy/docs/wrapping.html
+++ b/utils/jalopy/docs/wrapping.html
@@ -1,4 +1,21 @@
 
+
     
   
       
@@ -583,4 +600,4 @@ String[] constraints = {                                               |
 If both options are left disabled, the array elements will be printed in one
 line, right after the left curly brace.
 
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4.3.3. Indentation  Home  4.3.5. Blank Lines
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-            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
\ No newline at end of file
+            Copyright © 2001-2004, Marco Hunsicker. All rights reserved. Hosted by SourceForge.net
diff --git a/utils/jalopy/readme.html b/utils/jalopy/readme.html
index 45008c9..8b7cca1 100755
--- a/utils/jalopy/readme.html
+++ b/utils/jalopy/readme.html
@@ -1,4 +1,21 @@
 
+
       
    
JALOPY Java Source Code Formatter Beautifier Pretty Printer
Overview •
                     Download •
@@ -50,4 +67,4 @@ For a list of project contributors, see
 /docs/contributors.html.
 
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             Copyright © 2001-2002, Marco Hunsicker. All rights reserved.
-          
\ No newline at end of file
+          
-- 
1.7.10.2



Aliphatic/hydrophobic	ILVAM
Aromatic	FWY
Positive	KRH
Negative	DE
Hydrophilic	STNQ
conformationally special	PG
Cysteine	C

Aliphatic/hydrophobic	ILVAM
Aromatic	FWY
Positive	KRH
Negative	DE
Hydrophilic	STNQ
conformationally special	PG
Cysteine	C

A	Ala	Alanine	aliphatic - hydrophobic - neutral	GCT - GCC - GCA - GCG
B		either aspartic acid or asparagine
C	Cys	Cysteine	polar - hydrophobic - neutral	TGT - TGC
D	Asp	Aspartic Acid	polar - hydrophilic - charged (-)	GAT - GAC
E	Glu	Glutamic Acid	polar - hydrophilic - charged (-)	GAA - GAG
F	Phe	Phenylalanine	aromatic - hydrophobic - neutral	TTT - TTC
G	Gly	Glycine		GGT - GGC - GGA - GGG
H	His	Histidine	aromatic - polar - hydrophilic - charged (+)	CAT - CAC
I	Ile	Isoleucine	aliphatic - hydrophobic - neutral	ATT - ATC - ATA
K	Lys	Lysine		AAA - AAG
L	Leu	Leucine	aliphatic - hydrophobic - neutral	TTG - TTA - CTT - CTC - CTA - CTG
M	Met	Methionine	hydrophobic - neutral	ATG
N	Asn	Asparagine	polar - hydrophilic - neutral	AAT - AAC
P	Pro	Proline	hydrophobic - neutral	CCT - CCC - CCA - CCG
Q	Gln	Glutamine	polar - hydrophilic - neutral	CAA - CAG
R	Arg	Arginine	polar - hydrophilic - charged (+)	CGT - CGC - CGA - CGG - AGA - AGG
S	Ser	Serine	polar - hydrophilic - neutral	TCT - TCC - TCA - TCG - AGT - AGC
T	Thr	Threonine	polar - hydrophilic - neutral	ACT - ACC - ACA - ACG
V	Val	Valine	aliphatic - hydrophobic - neutral	GTT - GTC - GTA - GTG
W	Trp	Tryptophan	aromatic - hydrophobic - neutral	TGG
X		UNKNOWN
Y	Tyr	Tyrosine	aromatic - polar - hydrophobic	TAT - TAC
Z		either glutamic acid or glutamine
	End	Terminator		TAA - TAG - TGA

A	Ala	Alanine	aliphatic + hydrophobic + neutral	GCT + GCC + GCA + GCG
B		either aspartic acid or asparagine
C	Cys	Cysteine	polar + hydrophobic + neutral	TGT + TGC
D	Asp	Aspartic Acid	polar + hydrophilic + charged (-)	GAT + GAC
E	Glu	Glutamic Acid	polar + hydrophilic + charged (-)	GAA + GAG
F	Phe	Phenylalanine	aromatic + hydrophobic + neutral	TTT + TTC
G	Gly	Glycine		GGT + GGC + GGA + GGG
H	His	Histidine	aromatic + polar + hydrophilic + charged (+)	CAT + CAC
I	Ile	Isoleucine	aliphatic + hydrophobic + neutral	ATT + ATC + ATA
K	Lys	Lysine		AAA + AAG
L	Leu	Leucine	aliphatic + hydrophobic + neutral	TTG + TTA + CTT + CTC + CTA + CTG
M	Met	Methionine	hydrophobic + neutral	ATG
N	Asn	Asparagine	polar + hydrophilic + neutral	AAT + AAC
P	Pro	Proline	hydrophobic + neutral	CCT + CCC + CCA + CCG
Q	Gln	Glutamine	polar + hydrophilic + neutral	CAA + CAG
R	Arg	Arginine	polar + hydrophilic + charged (+)	CGT + CGC + CGA + CGG + AGA + AGG
S	Ser	Serine	polar + hydrophilic + neutral	TCT + TCC + TCA + TCG + AGT + AGC
T	Thr	Threonine	polar + hydrophilic + neutral	ACT + ACC + ACA + ACG
V	Val	Valine	aliphatic + hydrophobic + neutral	GTT + GTC + GTA + GTG
W	Trp	Tryptophan	aromatic + hydrophobic + neutral	TGG
X		UNKNOWN
Y	Tyr	Tyrosine	aromatic + polar + hydrophobic	TAT + TAC
Z		either glutamic acid or glutamine
	End	Terminator		TAA + TAG + TGA

Data Sharing Capability	Jalview Version
Alignments, sequences and annotation, trees, database - references, cDNA/protein mappings.	2.4
Mouseover location across linked DNA, protein and structure - positions.	2.4
Jalview project settings (Multiple views, groups, tree - partitions, colouring, window positions)	2.5
Sequence region and column selections	2.5

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11.3. License	Home	Appendix B. The Jalopy BSD License

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Appendix C. ANTLR SOFTWARE RIGHTS	Home	Appendix E. GNU GENERAL PUBLIC LICENSE Version 2, June 1991

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Appendix A. Library Dependencies	Home	Appendix C. ANTLR SOFTWARE RIGHTS

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Appendix F. GNU Free Documentation License Version 1.1, March 2000	Home	Appendix H. SUN PUBLIC LICENSE Version 1.0

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Appendix D. The Apache Software License, Version 1.1	Home	Appendix F. GNU Free Documentation License Version 1.1, March 2000

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Appendix G. Common Public License Version 1.0	Home	Bibliography

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8.2. Integration	Home	Chapter 9. JDeveloper Extension

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10.2. Integration	Home	Chapter 11. NetBeans/Sun ONE Studio module

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11.2. Integration	Home	Appendix A. Library Dependencies

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4.3.7. Imports	Home	4.3.9. Javadoc

Developing Jalview

Developing Jalview

The Genetic Code

U

C

A

G

U

C

A

G

The Genetic Code

U

C

A

G

U

C

A

G

Bibliography

Tabacaria

Initial beta version (2002-02-10)

Index

A

B

C

D

E

F

G

H

I

J

L

M

N

O

P

R

S

T

U

V

W

Plug-ins

4.3.5.3.2. Descriptions

4.3.5.3.3. Fill character

Chapter 3. Usage