From: amwaterhouse Date: Thu, 27 Jan 2005 18:41:17 +0000 (+0000) Subject: JavaHelp files added X-Git-Tag: Release_2_0~717 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bfbc6adb2123ba3e4c267384c0d39849f888c794;p=jalview.git JavaHelp files added --- diff --git a/help/help.hs b/help/help.hs new file mode 100755 index 0000000..afb009d --- /dev/null +++ b/help/help.hs @@ -0,0 +1,32 @@ + + + + + Jalview Documentation + + + home + + + + + TOC + Table Of Contents + javax.help.TOCView + helpTOC.xml + + + Index + Index + javax.help.IndexView + helpIndex.xml + + + Search + Search + javax.help.SearchView + + JavaHelpSearch + + + diff --git a/help/help.jhm b/help/help.jhm new file mode 100755 index 0000000..363ee88 --- /dev/null +++ b/help/help.jhm @@ -0,0 +1,23 @@ + + + + + + + + + + + + + + + + + + + + + + + diff --git a/help/helpIndex.xml b/help/helpIndex.xml new file mode 100755 index 0000000..7d62840 --- /dev/null +++ b/help/helpIndex.xml @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/help/helpTOC.xml b/help/helpTOC.xml new file mode 100755 index 0000000..c49436d --- /dev/null +++ b/help/helpTOC.xml @@ -0,0 +1,28 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/help/html/colourSchemes/colourSchemes.html b/help/html/colourSchemes/colourSchemes.html new file mode 100755 index 0000000..4264d38 --- /dev/null +++ b/help/html/colourSchemes/colourSchemes.html @@ -0,0 +1,325 @@ + + + +Untitled Document + + + + + +

Zappo Colours
+
+ The residues are coloured according to their physico-chemical properties as + follows:

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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

Taylor

These colours were invented by Willie Taylor and an entertaining description + of their birth can be found in Protein Engineering, Vol 10 , 743-746 (1997)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

A	V	I	L
M	F	Y	W
H	R	K	N
Q	E	D	S
T	G	P	C

Hydrophobicity

According to the hydrophobicity table of Kyte, J., and Doolittle, R.F., J. + Mol. Biol. 1157, 105-132, 1982. The most hydrophobic residues according to this + table are coloured red and the most hydrophilic ones are coloured blue.

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

I	V	L	F	C
M	A	G	X	T
S	W	Y	P	H
E	Z	Q	D	B
N	K	R

Helix Propensity

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

E	M	A	Z	L
K	F	Q	I	W
V	D	X	H	R
B	T	S	C	Y
N	G	P

Strand propensity

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

V	I	Y	F	W
L	T	C	Q	M
X	R	N	H	A
S	G	Z	K	B
P	D	E

Turn propensity

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

N	G	P	B	D
S	C	Y	K	X
Q	W	T	R	H
Z	E	A	F	M
L	V	I

Buried index

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

C	I	V	L	F
M	G	A	W	X
S	H	T	P	Y
N	B	D	Q	Z
E	R	K

Nucleotide Colours

+ + + + + + + +

Blosum62

Gaps are coloured white. If a residue matchs the consensus sequence residue + at that position it is colored dark blue. If it does not match the consensus + residue but the 2 residues have a positive Blosum62 score, it is colored light + blue.

Colouring above a percentage identity threshold
+ Selecting this option causes the colour scheme to be applied to only those residues + that occur in that column more than a certain percentage of the time. For instance + selecting the threshold to be 100 will only colour those columns with 100 % + identity. This threshold option can be applied to the Zappo, Taylor, Hydrophobicity + and User colour schemes.
+ This option depends on a consensus calculation having been performed. If no + consensus exists (e.g. after a copy or a clustalw alignment) then no residues + are coloured.

PID Colours
+ This depends on the applet having performed a consensus calculation on the alignment.
+ The PID option colours the residues (boxes and/or text) according to the percentage + of the residues in each column that agree with the consensus sequence. Only + the residues that agree with the consensus residue for each column are coloured.
+

+ + diff --git a/help/html/images/align.gif b/help/html/images/align.gif new file mode 100755 index 0000000..aa04b03 Binary files /dev/null and b/help/html/images/align.gif differ diff --git a/help/html/index.html b/help/html/index.html new file mode 100755 index 0000000..c9a98b0 --- /dev/null +++ b/help/html/index.html @@ -0,0 +1,14 @@ + + + +Untitled Document + + + + +

+ Jalview + Documentation

Your guide to Jalview

+ + diff --git a/help/html/menus/calculateMenu.html b/help/html/menus/calculateMenu.html new file mode 100755 index 0000000..f73d63c --- /dev/null +++ b/help/html/menus/calculateMenu.html @@ -0,0 +1,165 @@ + + + +Untitled Document + + + + +Calculate menu
+Consensus sequence
+Sorting sequence by pairwise identity to consensus
+Sorting by tree order
+Sorting by group order
+Removing redundancy of sequences
+Smith-Waterman pairwise alignment
+Principal component analysis
+UPGMA tree using percentage identity distances
+Neighbour joining tree using percentage identity distances
+Conservation
+
+Consensus sequence
+Each residue in the consensus sequence is the most frequent residue in each column +of the alignment excluding gap residues ' ','-' and '.' . You can't access the +consensus sequence directly but it is used in the PID colour scheme.
+When the editor first starts up the consensus sequence is automatically calculated +using all the sequences in the alignment and the PID colour scheme is used as +default. If the consensus option is selected again only the currently selected +sequences are used to calculate it and all sequences in the alignment are coloured +according to that consensus.
+

Sorting sequences
+ Once a consensus calculation has been done selecting this option will sort the + selected sequences by their percentage identity to the consensus sequence. The + most similar sequence is put at the top. If no sequences are selected then redundancy + is removed from the whole alignment.
+ Sorting by tree order
+ If a UPGMA tree or a neighbour joining tree has been displayed then the main + alignment window displays the sequences in the same order as they appear in + the tree. This makes for easier comparison of the tree and the alignment.
+
+ Sorting by group order
+ If the sequences have been grouped either by hand or by selecting a point on + the tree then this option will reorder the alignment so all sequences in the + same group are together. The largest group is shown at the top of the alignment + and the smallest at the bottom.
+ Removing redundancy
+ Selecting this option brings up a window asking you to select a threshold. If + the percentage identity between two sequences exceeds this value one of the + sequences (the shorter) is discarded. The redundancy calculation is done when + the Apply button is pressed. For large numbers of sequences this can take a + long time as all pairs have to be compared.
+ Pairwise alignment (Proteins only)
+ This calculation is performed on the selected sequences only. Java is not the + fastest language in the world and aligning more than a handful of sequences + will take a fair amount of time.
+ For each pair of sequences the best global alignment is found using BLOSUM62 + as the scoring matrix. The scores reported are the raw scores. The sequences + are aligned using a dynamic programming technique and using the following gap + penalties :

Gap open : 12
+ Gap extend : 2

When you select the pairwise alignment option a new window will come up which + will display the alignments in a text format as they are calculated. Also displayed + is information about the alignment such as alignment score, length and percentage + identity between the sequences.

If you want to save that pairwise alignment (it's not in any known format I'm + afraid) you can cut and paste it from the text window with the mouse. You can + also press the 'View in alignment editor' button to bring up another editor + window.
+

Principal Component Analysis
+ This is a method of clustering sequences based on the method developed by G. + Casari, C. Sander and A. Valencia. Structural Biology volume 2, no. 2, February + 1995 . Extra information can also be found at the SeqSpace server at the EBI. +
+ The version implemented here only looks at the clustering of whole sequences + and not individual positions in the alignment to help identify functional residues. + For large alignments plans are afoot to use the CORBA server written by Chris + Dodge to do this 'residue space' PCA remotely.

When the Calculate->Principal component analysis option is selected all + the sequences (not just the selected ones) are used in the calculation and for + large numbers of sequences this could take quite a time. When the calculation + is finished a new window is displayed showing the projections of the sequences + along the 2nd, 3rd and 4th vectors giving a 3dimensional view of how the sequences + cluster.

This 3d view can be rotated by holding the left mouse button down in the PCA + window and moving it. The user can also zoom in and out by using the up and + down arrow keys.

Individual points can be selected using the mouse and selected sequences show + up green in the PCA window and the usual grey background/white text in the alignment + and tree windows.

Different eigenvectors can be used to do the projection by changing the selected + dimensions in the 3 menus underneath the 3d window.
+

UPGMA tree
+ If this option is selected from the Calculate menu then all sequences are used + to generate a UPGMA tree. The pairwise distances used to cluster the sequences + are the percentage mismatch between two sequences. For a reliable phylogenetic + tree I recommend other programs (phylowin, phylip) should be used as they have + the speed to use better distance methods and bootstrapping. Again, plans are + afoot for a server to do this and to be able to read in tree files generated + by other programs.
+ When the tree has been calculated a new window is displayed showing the tree + with labels on the leaves showing the sequence ids. The user can select the + ids with the mouse and the selected sequences will also be selected in the alignment + window and the PCA window if that analysis has been calculated.

Selecting the 'show distances' checkbox will put branch lengths on the branches. + These branch lengths are the percentage mismatch between two nodes.

Postscript output can be generated for this tree and mailed to you by clicking + the Output button. This will bring up a window asking you for your email address + and you can set font options and the page orientation. Clicking the Apply button + will generate the postscript and send the email.
+

Neighbour Joining tree
+ The distances between sequences for this tree are generated in the same way + as for the UPGMA tree. The method of clustering is the neighbour joining method + which doesn't just pick the two closest leaves to cluster together but compensates + for long edges by subtracting from the distances the average distance from each + leaf to all the others.
+ Selection and output options are the same as for the UPGMA tree.

Conservation
+ This option is based on the AMAS method of multiple sequence alignment analysis + (Livingstone C.D. and Barton G.J. (1993), Protein Sequence Alignments: A Strategy + for the Hierarchical Analysis of Residue Conservation.CABIOS Vol. 9 No. 6 (745-756)). +
+ Hierarchical analysis is based on each residue having certain physico-chemical + properties listed as follows:
+
+
+
+

In brief go about it like this :
+

The alignment can first be divided into groups. This is best done by first + creating an average distance tree (Calculate->Average distance tree). Selecting + a position on the tree will cluster the sequences into groups depending on the + position selected. Each group is coloured a different colour which is used for + both the ids in the tree and alignment windows and the sequences themselves. + If a PCA window is visible a visual comparison can be made between the clustering + based on the tree and the PCA.
+ This link provides an example of the output after grouping for Pfam family rnaseH: +

The grouping by tree may not be satisfactory and the user may want to edit + the groups (Edit->Groups...) to put any outliers together.

Before selecting the conservation option change the colour scheme to something + sensible (Taylor or hydrophobicity for example). When the conservation is done + the existing colour scheme is modified so that the most conserved columns in + each group have the most intense colours and the least conserved are the palest. +

This link shows the results of first colouring the alignment by hydrophobicity + (Colour->by hydrophobicity) then performing conservation analysis (Calculate->Conservation). + Conserved hydrophobic columns are shown with predominately red residues and + conserved hydrophilic columns with blue. The most conserved regions have the + brightest colours.
+

+
+ Here is shown the same conservation but with Taylor colours instead of hydrophobicity + (Colour->Taylor).
+

The conservation analysis is done on each sequence group. This highlights differences + and similarities in conserved residue properties between groups.

+ + diff --git a/help/html/misc/aminoAcids.html b/help/html/misc/aminoAcids.html new file mode 100755 index 0000000..ca09346 --- /dev/null +++ b/help/html/misc/aminoAcids.html @@ -0,0 +1,172 @@ + + + +Untitled Document + + + + + + + +

+

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

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

+

+ + diff --git a/help/html/misc/geneticCode.html b/help/html/misc/geneticCode.html new file mode 100755 index 0000000..913de69 --- /dev/null +++ b/help/html/misc/geneticCode.html @@ -0,0 +1,337 @@ + + + +Untitled Document + + + + + + + +

The Genetic Code

+ + + + + + + + + + + +

2nd Position

1st Position

(5' end)

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

U

C

A

G

U

+ + + + + + + + + + + + +

Phe

Leu

+ + + + + + + + + + + + +

Ser

+ + + + + + + + + + + + +

Tyr

STOP

+ + + + + + + + + + + + +

Cys

STOP

Trp

+ + + + + + + + + + + + +

C

+ + + + + + + + + + + + +

Leu

+ + + + + + + + + + + + +

Pro

+ + + + + + + + + + + + +

His

Gln

+ + + + + + + + + + + + +

Arg

+ + + + + + + + + + + + +

A

+ + + + + + + + + + + + +

Ile

Met

+ + + + + + + + + + + + +

Thr

+ + + + + + + + + + + + +

Asn

Lys

+ + + + + + + + + + + + +

Ser

Arg

+ + + + + + + + + + + + +

G

+ + + + + + + + + + + + +

Val

+ + + + + + + + + + + + +

Ala

+ + + + + + + + + + + + +

Asp

Glu

+ + + + + + + + + + + + +

Gly

+ + + + + + + + + + + + +

3rd Position

(3'end)

+ + diff --git a/lib/jhall.jar b/lib/jhall.jar new file mode 100755 index 0000000..cb2e2f7 Binary files /dev/null and b/lib/jhall.jar differ diff --git a/lib/jhindexer b/lib/jhindexer new file mode 100755 index 0000000..e84a1b2 --- /dev/null +++ b/lib/jhindexer @@ -0,0 +1,49 @@ +#! /bin/sh +# This builds a search database + +# Cygwin support. $cygwin _must_ be set to either true or false. +case "`uname`" in + CYGWIN*) cygwin=true ;; + *) cygwin=false ;; +esac + +# For Cygwin, ensure paths are in UNIX format before anything is touched +if $cygwin; then + [ -n "$JAVAHELP_HOME" ] && + JAVAHELP_HOME=`cygpath --unix "$JAVAHELP_HOME"` +fi + +if [ "$JAVAHELP_HOME" = "" ] ; then + # try to find jhindexer + if [ -d /opt/javahelp ] ; then + JAVAHELP_HOME=/opt/javahelp + fi + + if [ -d ${HOME}/opt/jhindexer ] ; then + JAVAHELP_HOME=${HOME}/opt/javahelp + fi + + ## resolve links - $0 may be a link to javahelp's home + PRG=$0 + progname=`basename $0` + + while [ -h "$PRG" ] ; do + ls=`ls -ld "$PRG"` + link=`expr "$ls" : '.*-> $.*$$'` + if expr "$link" : '.*/.*' > /dev/null; then + PRG="$link" + else + PRG="`dirname $PRG`/$link" + fi + done + + JAVAHELP_HOME=`dirname "$PRG"`/../.. + +fi + +# For Cygwin, switch paths to Windows format before running java +if $cygwin; then + JAVAHELP_HOME=`cygpath --path --windows "$JAVAHELP_HOME"` +fi + +java -jar $JAVAHELP_HOME/javahelp/bin/jhindexer.jar "$@" diff --git a/lib/jhindexer.jar b/lib/jhindexer.jar new file mode 100755 index 0000000..5e54263 Binary files /dev/null and b/lib/jhindexer.jar differ