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Added MAFFT, minor fixes
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@4ment
4ment committed Nov 27, 2015
1 parent c655765 commit 4c863ce
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Showing 12 changed files with 139 additions and 53 deletions.
37 changes: 30 additions & 7 deletions Seqotron/Base.lproj/MFDocument.xib
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="7702" systemVersion="14D136" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none">
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="9060" systemVersion="15B42" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none">
<dependencies>
<deployment identifier="macosx"/>
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="7702"/>
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="9060"/>
</dependencies>
<objects>
<customObject id="-2" userLabel="File's Owner" customClass="MFWindowController">
Expand Down Expand Up @@ -52,6 +52,7 @@
<customView id="hdo-3w-UMQ">
<rect key="frame" x="0.0" y="373" width="87" height="20"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMinY="YES"/>
<animations/>
</customView>
<scrollView horizontalLineScroll="10" horizontalPageScroll="10" verticalLineScroll="10" verticalPageScroll="10" usesPredominantAxisScrolling="NO" horizontalScrollElasticity="none" verticalScrollElasticity="none" id="BPb-nj-GTp" customClass="MFSyncronizedScrollView">
<rect key="frame" x="0.0" y="0.0" width="87" height="373"/>
Expand All @@ -63,20 +64,26 @@
<view id="ZbT-9E-1O2" customClass="MFNamesView">
<rect key="frame" x="0.0" y="0.0" width="70" height="356"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" heightSizable="YES"/>
<animations/>
</view>
</subviews>
<animations/>
<color key="backgroundColor" name="controlBackgroundColor" catalog="System" colorSpace="catalog"/>
</clipView>
<animations/>
<scroller key="horizontalScroller" verticalHuggingPriority="750" horizontal="YES" id="FAz-8G-XVR">
<rect key="frame" x="1" y="357" width="45" height="15"/>
<rect key="frame" x="1" y="357" width="70" height="15"/>
<autoresizingMask key="autoresizingMask"/>
<animations/>
</scroller>
<scroller key="verticalScroller" verticalHuggingPriority="750" doubleValue="1" horizontal="NO" id="pcX-gl-PJw">
<rect key="frame" x="46" y="1" width="15" height="356"/>
<rect key="frame" x="71" y="1" width="15" height="356"/>
<autoresizingMask key="autoresizingMask"/>
<animations/>
</scroller>
</scrollView>
</subviews>
<animations/>
</customView>
<customView id="mum-UX-21V">
<rect key="frame" x="88" y="0.0" width="626" height="393"/>
Expand All @@ -92,29 +99,37 @@
<view id="pCY-JN-mce" customClass="MFSequencesView">
<rect key="frame" x="0.0" y="0.0" width="609" height="356"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" heightSizable="YES"/>
<animations/>
<connections>
<outlet property="delegate" destination="-2" id="tZt-sk-lli"/>
</connections>
</view>
</subviews>
<animations/>
<color key="backgroundColor" name="controlBackgroundColor" catalog="System" colorSpace="catalog"/>
</clipView>
<animations/>
<scroller key="horizontalScroller" verticalHuggingPriority="750" horizontal="YES" id="kHz-fh-Xqa">
<rect key="frame" x="1" y="357" width="427" height="15"/>
<rect key="frame" x="1" y="357" width="609" height="15"/>
<autoresizingMask key="autoresizingMask"/>
<animations/>
</scroller>
<scroller key="verticalScroller" verticalHuggingPriority="750" doubleValue="1" horizontal="NO" id="uRa-1b-6m6">
<rect key="frame" x="428" y="1" width="15" height="356"/>
<rect key="frame" x="610" y="1" width="15" height="356"/>
<autoresizingMask key="autoresizingMask"/>
<animations/>
</scroller>
</scrollView>
<customView id="40N-Q1-j0D" customClass="MFRulerView">
<rect key="frame" x="0.0" y="373" width="626" height="20"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMinY="YES"/>
<animations/>
</customView>
</subviews>
<animations/>
</customView>
</subviews>
<animations/>
<holdingPriorities>
<real value="250"/>
<real value="250"/>
Expand All @@ -124,8 +139,9 @@
</connections>
</splitView>
<textField horizontalHuggingPriority="251" verticalHuggingPriority="750" id="jjC-GQ-vGk">
<rect key="frame" x="7" y="4" width="479" height="14"/>
<rect key="frame" x="7" y="4" width="689" height="14"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMaxY="YES"/>
<animations/>
<textFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" sendsActionOnEndEditing="YES" title="Label" id="7nK-ro-BDd">
<font key="font" metaFont="system" size="10"/>
<color key="textColor" name="controlTextColor" catalog="System" colorSpace="catalog"/>
Expand All @@ -140,6 +156,7 @@
</connections>
</textField>
</subviews>
<animations/>
</view>
<toolbar key="toolbar" implicitIdentifier="457CAABD-8D24-4B72-85AD-2B0D5D01C752" autosavesConfiguration="NO" displayMode="iconAndLabel" sizeMode="regular" id="0C7-wv-z3D">
<allowedToolbarItems>
Expand All @@ -151,6 +168,7 @@
<popUpButton key="view" verticalHuggingPriority="750" id="HjY-EC-fiz">
<rect key="frame" x="0.0" y="14" width="100" height="25"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<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">
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
<font key="font" metaFont="menu"/>
Expand All @@ -176,6 +194,7 @@
<popUpButton key="view" id="K9x-e8-zGI">
<rect key="frame" x="0.0" y="9" width="100" height="25"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES" heightSizable="YES"/>
<animations/>
<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">
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
<font key="font" metaFont="menu"/>
Expand All @@ -201,6 +220,7 @@
<popUpButton key="view" verticalHuggingPriority="750" id="Dia-Ep-hUU">
<rect key="frame" x="0.0" y="14" width="100" height="25"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<popUpButtonCell key="cell" type="roundTextured" bezelStyle="texturedRounded" alignment="left" lineBreakMode="truncatingTail" borderStyle="border" imageScaling="proportionallyDown" inset="2" autoenablesItems="NO" id="8YA-wp-1Pm">
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
<font key="font" metaFont="menu"/>
Expand All @@ -227,6 +247,7 @@
<searchField key="view" wantsLayer="YES" verticalHuggingPriority="750" tag="999" id="ivq-8Q-qCO">
<rect key="frame" x="0.0" y="14" width="96" height="22"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<searchFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" selectable="YES" editable="YES" borderStyle="bezel" usesSingleLineMode="YES" bezelStyle="round" sendsWholeSearchString="YES" id="P5l-Pp-tAF">
<font key="font" metaFont="system"/>
<color key="textColor" name="controlTextColor" catalog="System" colorSpace="catalog"/>
Expand Down Expand Up @@ -266,6 +287,7 @@
<comboBox verticalHuggingPriority="750" id="efM-qq-rof">
<rect key="frame" x="20" y="16" width="239" height="26"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<comboBoxCell key="cell" scrollable="YES" lineBreakMode="clipping" selectable="YES" sendsActionOnEndEditing="YES" borderStyle="bezel" drawsBackground="YES" completes="NO" numberOfVisibleItems="5" id="sIy-ZL-epa">
<font key="font" metaFont="system"/>
<color key="textColor" name="controlTextColor" catalog="System" colorSpace="catalog"/>
Expand All @@ -283,6 +305,7 @@
</comboBoxCell>
</comboBox>
</subviews>
<animations/>
</customView>
<userDefaultsController representsSharedInstance="YES" id="7nc-Tq-vut"/>
<arrayController id="aPM-8k-Gsk" userLabel="Genetic Codes Controller">
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24 changes: 20 additions & 4 deletions Seqotron/MFAligner.xib
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="7702" systemVersion="14D136" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none" customObjectInstantitationMethod="direct">
<document type="com.apple.InterfaceBuilder3.Cocoa.XIB" version="3.0" toolsVersion="9059" systemVersion="15B42" targetRuntime="MacOSX.Cocoa" propertyAccessControl="none" customObjectInstantitationMethod="direct">
<dependencies>
<deployment identifier="macosx"/>
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="7702"/>
<plugIn identifier="com.apple.InterfaceBuilder.CocoaPlugin" version="9059"/>
</dependencies>
<objects>
<customObject id="-2" userLabel="File's Owner" customClass="MFAlignerController">
Expand All @@ -24,6 +24,7 @@
<tabView id="Pjs-bF-H4M">
<rect key="frame" x="-8" y="97" width="496" height="179"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" flexibleMinY="YES" heightSizable="YES"/>
<animations/>
<font key="font" metaFont="system"/>
<tabViewItems>
<tabViewItem label="Muscle" identifier="1" id="jH2-kv-zsg">
Expand All @@ -34,8 +35,9 @@
<matrix verticalHuggingPriority="750" allowsEmptySelection="NO" autorecalculatesCellSize="YES" id="F8b-0Z-0MZ">
<rect key="frame" x="29" y="74" width="298" height="18"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<color key="backgroundColor" name="controlColor" catalog="System" colorSpace="catalog"/>
<size key="cellSize" width="125" height="18"/>
<size key="cellSize" width="124" height="18"/>
<size key="intercellSpacing" width="4" height="2"/>
<buttonCell key="prototype" type="radio" title="Radio" imagePosition="left" alignment="left" inset="2" id="ZRr-rC-iDk">
<behavior key="behavior" changeContents="YES" doesNotDimImage="YES" lightByContents="YES"/>
Expand All @@ -60,6 +62,14 @@
</connections>
</matrix>
</subviews>
<animations/>
</view>
</tabViewItem>
<tabViewItem label="MAFFT" identifier="" id="0Tk-EM-xJv">
<view key="view" id="swz-Bt-zbr">
<rect key="frame" x="10" y="33" width="476" height="133"/>
<autoresizingMask key="autoresizingMask" widthSizable="YES" heightSizable="YES"/>
<animations/>
</view>
</tabViewItem>
</tabViewItems>
Expand All @@ -70,6 +80,7 @@
<button verticalHuggingPriority="750" id="sjF-mz-WJm">
<rect key="frame" x="390" y="-1" width="71" height="32"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<buttonCell key="cell" type="push" title="Align" bezelStyle="rounded" alignment="center" borderStyle="border" imageScaling="proportionallyDown" inset="2" id="eKf-hI-wII">
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
<font key="font" metaFont="system"/>
Expand All @@ -84,6 +95,7 @@ DQ
<button verticalHuggingPriority="750" id="XU9-Tu-ylK">
<rect key="frame" x="308" y="-1" width="83" height="32"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<buttonCell key="cell" type="push" title="Cancel" bezelStyle="rounded" alignment="center" borderStyle="border" imageScaling="proportionallyDown" inset="2" id="h4k-2y-61t">
<behavior key="behavior" pushIn="YES" lightByBackground="YES" lightByGray="YES"/>
<font key="font" metaFont="system"/>
Expand All @@ -98,18 +110,20 @@ Gw
<button id="bL3-FU-phd">
<rect key="frame" x="24" y="40" width="153" height="18"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<buttonCell key="cell" type="check" title="Translation alignment" bezelStyle="regularSquare" imagePosition="left" inset="2" id="YoG-Jr-0bM">
<behavior key="behavior" changeContents="YES" doesNotDimImage="YES" lightByContents="YES"/>
<font key="font" metaFont="system"/>
</buttonCell>
<connections>
<binding destination="-2" name="enabled" keyPath="self.transalignEnabled" id="dHA-dJ-Vr9"/>
<binding destination="-2" name="value" keyPath="self.transalign" id="J5I-aC-SER"/>
<binding destination="-2" name="enabled" keyPath="self.transalignEnabled" id="dHA-dJ-Vr9"/>
</connections>
</button>
<textField horizontalHuggingPriority="251" verticalHuggingPriority="750" id="SMi-9o-jgm">
<rect key="frame" x="24" y="73" width="116" height="17"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<textFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" sendsActionOnEndEditing="YES" title="Additional options" id="GPc-bX-YwA">
<font key="font" metaFont="system"/>
<color key="textColor" name="labelColor" catalog="System" colorSpace="catalog"/>
Expand All @@ -119,6 +133,7 @@ Gw
<textField verticalHuggingPriority="750" id="Eta-si-lYC">
<rect key="frame" x="152" y="73" width="287" height="22"/>
<autoresizingMask key="autoresizingMask" flexibleMaxX="YES" flexibleMinY="YES"/>
<animations/>
<textFieldCell key="cell" scrollable="YES" lineBreakMode="clipping" selectable="YES" editable="YES" sendsActionOnEndEditing="YES" state="on" borderStyle="bezel" drawsBackground="YES" id="0kf-D8-i4H">
<font key="font" metaFont="system"/>
<color key="textColor" name="textColor" catalog="System" colorSpace="catalog"/>
Expand All @@ -133,6 +148,7 @@ Gw
</connections>
</textField>
</subviews>
<animations/>
</view>
<connections>
<outlet property="delegate" destination="-2" id="EVV-dq-hgh"/>
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