1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
|
<?xml version="1.1" encoding="UTF-8" ?>
<Form version="1.3" maxVersion="1.7" type="org.netbeans.modules.form.forminfo.JFrameFormInfo">
<Properties>
<Property name="defaultCloseOperation" type="int" value="2"/>
<Property name="title" type="java.lang.String" value="About BRIG"/>
</Properties>
<SyntheticProperties>
<SyntheticProperty name="formSizePolicy" type="int" value="1"/>
</SyntheticProperties>
<AuxValues>
<AuxValue name="FormSettings_autoResourcing" type="java.lang.Integer" value="0"/>
<AuxValue name="FormSettings_autoSetComponentName" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_generateFQN" type="java.lang.Boolean" value="true"/>
<AuxValue name="FormSettings_generateMnemonicsCode" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_i18nAutoMode" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_layoutCodeTarget" type="java.lang.Integer" value="1"/>
<AuxValue name="FormSettings_listenerGenerationStyle" type="java.lang.Integer" value="0"/>
<AuxValue name="FormSettings_variablesLocal" type="java.lang.Boolean" value="false"/>
<AuxValue name="FormSettings_variablesModifier" type="java.lang.Integer" value="2"/>
</AuxValues>
<Layout>
<DimensionLayout dim="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" attributes="0">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" attributes="0">
<EmptySpace min="49" pref="49" max="-2" attributes="0"/>
<Group type="103" groupAlignment="0" attributes="0">
<Component id="versionLabel" alignment="0" min="-2" max="-2" attributes="0"/>
<Group type="102" alignment="1" attributes="0">
<Component id="jLabel2" min="-2" max="-2" attributes="0"/>
<EmptySpace pref="302" max="32767" attributes="0"/>
<Component id="jButton1" min="-2" max="-2" attributes="0"/>
</Group>
</Group>
</Group>
<Group type="102" alignment="0" attributes="0">
<EmptySpace max="-2" attributes="0"/>
<Component id="jScrollPane1" pref="568" max="32767" attributes="0"/>
</Group>
</Group>
<EmptySpace max="-2" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
<DimensionLayout dim="1">
<Group type="103" groupAlignment="0" attributes="0">
<Group type="102" alignment="0" attributes="0">
<EmptySpace max="-2" attributes="0"/>
<Component id="versionLabel" min="-2" max="-2" attributes="0"/>
<EmptySpace max="-2" attributes="0"/>
<Group type="103" groupAlignment="3" attributes="0">
<Component id="jLabel2" alignment="3" min="-2" max="-2" attributes="0"/>
<Component id="jButton1" alignment="3" min="-2" max="-2" attributes="0"/>
</Group>
<EmptySpace max="-2" attributes="0"/>
<Component id="jScrollPane1" pref="479" max="32767" attributes="0"/>
<EmptySpace min="-2" max="-2" attributes="0"/>
</Group>
</Group>
</DimensionLayout>
</Layout>
<SubComponents>
<Component class="javax.swing.JButton" name="jButton1">
<Properties>
<Property name="text" type="java.lang.String" value="OK"/>
</Properties>
<Events>
<EventHandler event="actionPerformed" listener="java.awt.event.ActionListener" parameters="java.awt.event.ActionEvent" handler="jButton1ActionPerformed"/>
</Events>
</Component>
<Component class="javax.swing.JLabel" name="versionLabel">
<Properties>
<Property name="text" type="java.lang.String" value="Blast Ring Image Generator (BRIG) Version 0.81"/>
</Properties>
</Component>
<Component class="javax.swing.JLabel" name="jLabel2">
<Properties>
<Property name="text" type="java.lang.String" value="Copyright Nabil Alikhan. 2010-2011."/>
</Properties>
</Component>
<Container class="javax.swing.JScrollPane" name="jScrollPane1">
<AuxValues>
<AuxValue name="autoScrollPane" type="java.lang.Boolean" value="true"/>
</AuxValues>
<Layout class="org.netbeans.modules.form.compat2.layouts.support.JScrollPaneSupportLayout"/>
<SubComponents>
<Component class="javax.swing.JTextArea" name="jTextArea1">
<Properties>
<Property name="columns" type="int" value="20"/>
<Property name="lineWrap" type="boolean" value="true"/>
<Property name="rows" type="int" value="5"/>
<Property name="text" type="java.lang.String" value="This java application can produce CGView rendered circular genome images 
based on BLAST output.

BRIG supports:
* Genbank/EMBL
* FASTA nucleotide; single entry or Multi-FASTA
* FASTA protein; single entry of Multi-FASTA

CHANGE-LOG
Version 0.80
* Now supports multi-fasta as reference, including protein files (BRIG will ask if you want spacers between Multi-fasta entries)
* BRIG asks if genbank reference is protein or nucleotide.
* BRIG doesn't let you do things like run BLASTP on genbank-nucleotide reference.
* Brig checks for existing BLAST results exist before running blast. (you can override 
 with Re-DO blast check.
* Fixed custom-annotation colour error
* Ability to change output image filename
* Fixed legend not showing colour when thresholds are off
* You can set minimum % identity in BRIG options (cannot be greater than other
 threshold values through)
* You can set a default set of colours in BRIG options
* Renamed “Reference sequence” labels
* Made it possible to change the order of rings
* Added ability to save a "PROFILE" (brig configurations but no data)
* Fix custom annotation errors/interface.
* Add ability to annotate spacers from multi-fasta 
* Handle Filenames with spacers.
* Fixed minor interface bugs"/>
</Properties>
</Component>
</SubComponents>
</Container>
</SubComponents>
</Form>
|
