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Added MAFFT, minor fixes
1 parent c655765 commit 4c863ce

12 files changed

+139
-53
lines changed

‎Seqotron/Base.lproj/MFDocument.xib‎

Lines changed: 30 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
2-
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="7702" systemVersion="14D136" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none">
2+
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="9060" systemVersion="15B42" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none">
33
<dependencies>
44
<deployment identifier="macosx"/>
5-
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="7702"/>
5+
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="9060"/>
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</dependencies>
77
<objects>
88
<customObject id="-2" userLabel="File's Owner" customClass="MFWindowController">
@@ -52,6 +52,7 @@
5252
<customView id="hdo-3w-UMQ">
5353
<rect key="frame" x="0.0" y="373" width="87" height="20"/>
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<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMinY="YES"/>
55+
<animations/>
5556
</customView>
5657
<scrollView horizontalLineScroll="10" horizontalPageScroll="10" verticalLineScroll="10" verticalPageScroll="10" usesPredominantAxisScrolling="NO" horizontalScrollElasticity="none" verticalScrollElasticity="none" id="BPb-nj-GTp" customClass="MFSyncronizedScrollView">
5758
<rect key="frame" x="0.0" y="0.0" width="87" height="373"/>
@@ -63,20 +64,26 @@
6364
<view id="ZbT-9E-1O2" customClass="MFNamesView">
6465
<rect key="frame" x="0.0" y="0.0" width="70" height="356"/>
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<autoresizingMask key="autoresizingMask" widthSizable="YES" heightSizable="YES"/>
67+
<animations/>
6668
</view>
6769
</subviews>
70+
<animations/>
6871
<color key="backgroundColor" name="controlBackgroundColor" catalog="System" colorSpace="catalog"/>
6972
</clipView>
73+
<animations/>
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<scroller key="horizontalScroller" verticalHuggingPriority="750" horizontal="YES" id="FAz-8G-XVR">
71-
<rect key="frame" x="1" y="357" width="45" height="15"/>
75+
<rect key="frame" x="1" y="357" width="70" height="15"/>
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<autoresizingMask key="autoresizingMask"/>
77+
<animations/>
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</scroller>
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<scroller key="verticalScroller" verticalHuggingPriority="750" doubleValue="1" horizontal="NO" id="pcX-gl-PJw">
75-
<rect key="frame" x="46" y="1" width="15" height="356"/>
80+
<rect key="frame" x="71" y="1" width="15" height="356"/>
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<autoresizingMask key="autoresizingMask"/>
82+
<animations/>
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</scroller>
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</scrollView>
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</subviews>
86+
<animations/>
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</customView>
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<customView id="mum-UX-21V">
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<rect key="frame" x="88" y="0.0" width="626" height="393"/>
@@ -92,29 +99,37 @@
9299
<view id="pCY-JN-mce" customClass="MFSequencesView">
93100
<rect key="frame" x="0.0" y="0.0" width="609" height="356"/>
94101
<autoresizingMask key="autoresizingMask" widthSizable="YES" heightSizable="YES"/>
102+
<animations/>
95103
<connections>
96104
<outlet property="delegate" destination="-2" id="tZt-sk-lli"/>
97105
</connections>
98106
</view>
99107
</subviews>
108+
<animations/>
100109
<color key="backgroundColor" name="controlBackgroundColor" catalog="System" colorSpace="catalog"/>
101110
</clipView>
111+
<animations/>
102112
<scroller key="horizontalScroller" verticalHuggingPriority="750" horizontal="YES" id="kHz-fh-Xqa">
103-
<rect key="frame" x="1" y="357" width="427" height="15"/>
113+
<rect key="frame" x="1" y="357" width="609" height="15"/>
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<autoresizingMask key="autoresizingMask"/>
115+
<animations/>
105116
</scroller>
106117
<scroller key="verticalScroller" verticalHuggingPriority="750" doubleValue="1" horizontal="NO" id="uRa-1b-6m6">
107-
<rect key="frame" x="428" y="1" width="15" height="356"/>
118+
<rect key="frame" x="610" y="1" width="15" height="356"/>
108119
<autoresizingMask key="autoresizingMask"/>
120+
<animations/>
109121
</scroller>
110122
</scrollView>
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<customView id="40N-Q1-j0D" customClass="MFRulerView">
112124
<rect key="frame" x="0.0" y="373" width="626" height="20"/>
113125
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMinY="YES"/>
126+
<animations/>
114127
</customView>
115128
</subviews>
129+
<animations/>
116130
</customView>
117131
</subviews>
132+
<animations/>
118133
<holdingPriorities>
119134
<real value="250"/>
120135
<real value="250"/>
@@ -124,8 +139,9 @@
124139
</connections>
125140
</splitView>
126141
<textField horizontalHuggingPriority="251" verticalHuggingPriority="750" id="jjC-GQ-vGk">
127-
<rect key="frame" x="7" y="4" width="479" height="14"/>
142+
<rect key="frame" x="7" y="4" width="689" height="14"/>
128143
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMaxY="YES"/>
144+
<animations/>
129145
<textFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" sendsActionOnEndEditing="YES" title="Label" id="7nK-ro-BDd">
130146
<font key="font" metaFont="system" size="10"/>
131147
<color key="textColor" name="controlTextColor" catalog="System" colorSpace="catalog"/>
@@ -140,6 +156,7 @@
140156
</connections>
141157
</textField>
142158
</subviews>
159+
<animations/>
143160
</view>
144161
<toolbar key="toolbar" implicitIdentifier="457CAABD-8D24-4B72-85AD-2B0D5D01C752" autosavesConfiguration="NO" displayMode="iconAndLabel" sizeMode="regular" id="0C7-wv-z3D">
145162
<allowedToolbarItems>
@@ -151,6 +168,7 @@
151168
<popUpButton key="view" verticalHuggingPriority="750" id="HjY-EC-fiz">
152169
<rect key="frame" x="0.0" y="14" width="100" height="25"/>
153170
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
171+
<animations/>
154172
<popUpButtonCell key="cell" type="roundTextured" title="Item 1" bezelStyle="texturedRounded" alignment="left" lineBreakMode="truncatingTail" state="on" borderStyle="border" imageScaling="proportionallyDown" inset="2" selectedItem="siT-es-2Ow" id="oS1-TT-laI">
155173
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
156174
<font key="font" metaFont="menu"/>
@@ -176,6 +194,7 @@
176194
<popUpButton key="view" id="K9x-e8-zGI">
177195
<rect key="frame" x="0.0" y="9" width="100" height="25"/>
178196
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES" heightSizable="YES"/>
197+
<animations/>
179198
<popUpButtonCell key="cell" type="roundTextured" bezelStyle="texturedRounded" alignment="left" lineBreakMode="truncatingTail" state="on" borderStyle="border" imageScaling="proportionallyDown" inset="2" autoenablesItems="NO" selectedItem="Yxy-nH-pUn" id="hZ4-Fq-tD9">
180199
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
181200
<font key="font" metaFont="menu"/>
@@ -201,6 +220,7 @@
201220
<popUpButton key="view" verticalHuggingPriority="750" id="Dia-Ep-hUU">
202221
<rect key="frame" x="0.0" y="14" width="100" height="25"/>
203222
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
223+
<animations/>
204224
<popUpButtonCell key="cell" type="roundTextured" bezelStyle="texturedRounded" alignment="left" lineBreakMode="truncatingTail" borderStyle="border" imageScaling="proportionallyDown" inset="2" autoenablesItems="NO" id="8YA-wp-1Pm">
205225
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
206226
<font key="font" metaFont="menu"/>
@@ -227,6 +247,7 @@
227247
<searchField key="view" wantsLayer="YES" verticalHuggingPriority="750" tag="999" id="ivq-8Q-qCO">
228248
<rect key="frame" x="0.0" y="14" width="96" height="22"/>
229249
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
250+
<animations/>
230251
<searchFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" selectable="YES" editable="YES" borderStyle="bezel" usesSingleLineMode="YES" bezelStyle="round" sendsWholeSearchString="YES" id="P5l-Pp-tAF">
231252
<font key="font" metaFont="system"/>
232253
<color key="textColor" name="controlTextColor" catalog="System" colorSpace="catalog"/>
@@ -266,6 +287,7 @@
266287
<comboBox verticalHuggingPriority="750" id="efM-qq-rof">
267288
<rect key="frame" x="20" y="16" width="239" height="26"/>
268289
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
290+
<animations/>
269291
<comboBoxCell key="cell" scrollable="YES" lineBreakMode="clipping" selectable="YES" sendsActionOnEndEditing="YES" borderStyle="bezel" drawsBackground="YES" completes="NO" numberOfVisibleItems="5" id="sIy-ZL-epa">
270292
<font key="font" metaFont="system"/>
271293
<color key="textColor" name="controlTextColor" catalog="System" colorSpace="catalog"/>
@@ -283,6 +305,7 @@
283305
</comboBoxCell>
284306
</comboBox>
285307
</subviews>
308+
<animations/>
286309
</customView>
287310
<userDefaultsController representsSharedInstance="YES" id="7nc-Tq-vut"/>
288311
<arrayController id="aPM-8k-Gsk" userLabel="Genetic Codes Controller">

‎Seqotron/MFAligner.xib‎

Lines changed: 20 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,8 +1,8 @@
11
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
2-
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="7702" systemVersion="14D136" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none" customObjectInstantitationMethod="direct">
2+
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="9059" systemVersion="15B42" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none" customObjectInstantitationMethod="direct">
33
<dependencies>
44
<deployment identifier="macosx"/>
5-
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="7702"/>
5+
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="9059"/>
66
</dependencies>
77
<objects>
88
<customObject id="-2" userLabel="File's Owner" customClass="MFAlignerController">
@@ -24,6 +24,7 @@
2424
<tabView id="Pjs-bF-H4M">
2525
<rect key="frame" x="-8" y="97" width="496" height="179"/>
2626
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMinY="YES" heightSizable="YES"/>
27+
<animations/>
2728
<font key="font" metaFont="system"/>
2829
<tabViewItems>
2930
<tabViewItem label="Muscle" identifier="1" id="jH2-kv-zsg">
@@ -34,8 +35,9 @@
3435
<matrix verticalHuggingPriority="750" allowsEmptySelection="NO" autorecalculatesCellSize="YES" id="F8b-0Z-0MZ">
3536
<rect key="frame" x="29" y="74" width="298" height="18"/>
3637
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
38+
<animations/>
3739
<color key="backgroundColor" name="controlColor" catalog="System" colorSpace="catalog"/>
38-
<size key="cellSize" width="125" height="18"/>
40+
<size key="cellSize" width="124" height="18"/>
3941
<size key="intercellSpacing" width="4" height="2"/>
4042
<buttonCell key="prototype" type="radio" title="Radio" imagePosition="left" alignment="left" inset="2" id="ZRr-rC-iDk">
4143
<behavior key="behavior" changeContents="YES" doesNotDimImage="YES" lightByContents="YES"/>
@@ -60,6 +62,14 @@
6062
</connections>
6163
</matrix>
6264
</subviews>
65+
<animations/>
66+
</view>
67+
</tabViewItem>
68+
<tabViewItem label="MAFFT" identifier="" id="0Tk-EM-xJv">
69+
<view key="view" id="swz-Bt-zbr">
70+
<rect key="frame" x="10" y="33" width="476" height="133"/>
71+
<autoresizingMask key="autoresizingMask" widthSizable="YES" heightSizable="YES"/>
72+
<animations/>
6373
</view>
6474
</tabViewItem>
6575
</tabViewItems>
@@ -70,6 +80,7 @@
7080
<button verticalHuggingPriority="750" id="sjF-mz-WJm">
7181
<rect key="frame" x="390" y="-1" width="71" height="32"/>
7282
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
83+
<animations/>
7384
<buttonCell key="cell" type="push" title="Align" bezelStyle="rounded" alignment="center" borderStyle="border" imageScaling="proportionallyDown" inset="2" id="eKf-hI-wII">
7485
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
7586
<font key="font" metaFont="system"/>
@@ -84,6 +95,7 @@ DQ
8495
<button verticalHuggingPriority="750" id="XU9-Tu-ylK">
8596
<rect key="frame" x="308" y="-1" width="83" height="32"/>
8697
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
98+
<animations/>
8799
<buttonCell key="cell" type="push" title="Cancel" bezelStyle="rounded" alignment="center" borderStyle="border" imageScaling="proportionallyDown" inset="2" id="h4k-2y-61t">
88100
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
89101
<font key="font" metaFont="system"/>
@@ -98,18 +110,20 @@ Gw
98110
<button id="bL3-FU-phd">
99111
<rect key="frame" x="24" y="40" width="153" height="18"/>
100112
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
113+
<animations/>
101114
<buttonCell key="cell" type="check" title="Translation alignment" bezelStyle="regularSquare" imagePosition="left" inset="2" id="YoG-Jr-0bM">
102115
<behavior key="behavior" changeContents="YES" doesNotDimImage="YES" lightByContents="YES"/>
103116
<font key="font" metaFont="system"/>
104117
</buttonCell>
105118
<connections>
106-
<binding destination="-2" name="enabled" keyPath="self.transalignEnabled" id="dHA-dJ-Vr9"/>
107119
<binding destination="-2" name="value" keyPath="self.transalign" id="J5I-aC-SER"/>
120+
<binding destination="-2" name="enabled" keyPath="self.transalignEnabled" id="dHA-dJ-Vr9"/>
108121
</connections>
109122
</button>
110123
<textField horizontalHuggingPriority="251" verticalHuggingPriority="750" id="SMi-9o-jgm">
111124
<rect key="frame" x="24" y="73" width="116" height="17"/>
112125
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
126+
<animations/>
113127
<textFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" sendsActionOnEndEditing="YES" title="Additional options" id="GPc-bX-YwA">
114128
<font key="font" metaFont="system"/>
115129
<color key="textColor" name="labelColor" catalog="System" colorSpace="catalog"/>
@@ -119,6 +133,7 @@ Gw
119133
<textField verticalHuggingPriority="750" id="Eta-si-lYC">
120134
<rect key="frame" x="152" y="73" width="287" height="22"/>
121135
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
136+
<animations/>
122137
<textFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" selectable="YES" editable="YES" sendsActionOnEndEditing="YES" state="on" borderStyle="bezel" drawsBackground="YES" id="0kf-D8-i4H">
123138
<font key="font" metaFont="system"/>
124139
<color key="textColor" name="textColor" catalog="System" colorSpace="catalog"/>
@@ -133,6 +148,7 @@ Gw
133148
</connections>
134149
</textField>
135150
</subviews>
151+
<animations/>
136152
</view>
137153
<connections>
138154
<outlet property="delegate" destination="-2" id="EVV-dq-hgh"/>

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